Variant report

Variant	rs600220
Chromosome Location	chr18:218285-218286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:217692-218538	Hela-S3	cervix:	n/a	n/a
2	NR2F2	chr18:217870-218310	K562	blood:	n/a	n/a
3	POLR2A	chr18:217410-219008	HepG2	liver:	n/a	n/a
4	POLR2A	chr18:217905-218434	HepG2	liver:	n/a	n/a
5	POLR2A	chr18:218241-218672	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr18:217456-219056	K562	blood:	n/a	n/a
7	POLR2A	chr18:218262-218613	GM12878	blood:	n/a	n/a
8	POLR2A	chr18:216231-219085	K562	blood:	n/a	n/a
9	POLR2A	chr18:218185-218681	HL-60	blood:	n/a	n/a
10	POLR2A	chr18:217397-218387	GM12892	blood:	n/a	n/a
11	POLR2A	chr18:218154-218375	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:217396-219638	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr18:217526-219005	A549	lung:	n/a	n/a
14	POLR2A	chr18:217555-218814	K562	blood:	n/a	n/a
15	POLR2A	chr18:217420-218692	K562	blood:	n/a	n/a
16	HNF4A	chr18:218077-218302	HepG2	liver:	n/a	chr18:218142-218157 chr18:218088-218103
17	POLR2A	chr18:217678-219005	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr18:218255-218301	K562	blood:	n/a	n/a

Variant related genes	Relation type
THOC1	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs12960837	0.83[ASN][1000 genomes]
rs1299113	0.96[ASN][1000 genomes]
rs1784380	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1785049	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2509447	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs471274	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs477066	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs481077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484863	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489560	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs489577	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs490425	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs513402	0.94[ASN][1000 genomes]
rs513894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs514003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs523239	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs535992	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs545447	0.96[ASN][1000 genomes]
rs557249	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577454	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs579219	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585578	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs598300	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs599361	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs600022	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs605826	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs620380	0.82[CHB][hapmap]
rs620837	0.82[CHB][hapmap]
rs620970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621782	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631343	1.00[CEU][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644438	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs655781	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs663186	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs672856	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7238463	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7241427	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064673	chr18:11543-249310	Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1061730	chr18:11543-322183	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1059645	chr18:11543-326679	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv576227	chr18:52933-322183	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1064150	chr18:99036-321710	Genic enhancers Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1055303	chr18:112328-304352	Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv543527	chr18:112328-304352	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv543530	chr18:112528-932674	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
9	nsv1067102	chr18:112528-984688	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
10	nsv543531	chr18:112528-984688	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
11	nsv1066441	chr18:136228-249310	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv1057029	chr18:141491-356238	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1066995	chr18:141491-415027	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv1064735	chr18:141491-483651	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
15	nsv1062680	chr18:141491-549166	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv1067218	chr18:141491-603796	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
17	nsv543544	chr18:141491-675519	Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
18	nsv1064998	chr18:141491-1095845	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
19	nsv543545	chr18:141491-1095845	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
20	nsv1057105	chr18:143546-235928	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
21	nsv531216	chr18:148763-293736	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
22	nsv532441	chr18:148763-1108997	Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
23	nsv530373	chr18:148963-533693	Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
24	nsv482910	chr18:161390-305010	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
25	nsv518642	chr18:196829-331506	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:160200-218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr18:193200-218800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr18:193400-227000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr18:193800-219200	Strong transcription	Primary T helper cells PMA-I stimulated	--
5	chr18:195200-231200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr18:195400-219000	Strong transcription	Primary T cells from cord blood	blood
7	chr18:195400-219000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr18:195400-219800	Strong transcription	Primary B cells from peripheral blood	blood
9	chr18:195400-220600	Strong transcription	Dnd41	blood
10	chr18:195400-228000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr18:195400-233000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:199800-251000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr18:205000-219200	Strong transcription	HMEC	breast
14	chr18:206000-220800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr18:206400-222200	Weak transcription	Fetal Brain Male	brain
16	chr18:208000-219000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr18:208400-218600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr18:208400-218800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr18:208600-218600	Strong transcription	Left Ventricle	heart
20	chr18:208800-227200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr18:209000-218800	Strong transcription	HSMM	muscle
22	chr18:209000-220800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr18:209200-218600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr18:209200-218800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr18:209200-219000	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr18:209200-219000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr18:209200-220400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr18:209200-220400	Strong transcription	Placenta	Placenta
29	chr18:209200-220600	Strong transcription	Adipose Nuclei	Adipose
30	chr18:209200-228200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr18:209400-219000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:209400-219200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr18:209400-219200	Strong transcription	Fetal Thymus	thymus
34	chr18:209400-219200	Strong transcription	K562	blood
35	chr18:209400-219400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:209400-230000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr18:209400-230000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr18:209600-218600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr18:209600-219000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr18:209600-220400	Strong transcription	A549	lung
41	chr18:209800-218600	Strong transcription	NHDF-Ad	bronchial
42	chr18:209800-219000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr18:209800-219200	Strong transcription	Primary B cells from cord blood	blood
44	chr18:209800-219400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr18:210200-218600	Strong transcription	Brain Germinal Matrix	brain
46	chr18:210200-218800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr18:210200-228000	Strong transcription	Osteobl	bone
48	chr18:210400-219000	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr18:210400-219000	Strong transcription	Fetal Muscle Leg	muscle
50	chr18:210400-219000	Strong transcription	Stomach Smooth Muscle	stomach

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