Variant report

Variant	rs10181000
Chromosome Location	chr2:98950659-98950660
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	TCF12	chr2:98950621-98951729	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:98950435-98951405	U87	brain:	n/a	n/a
3	TCF12	chr2:98950544-98951816	SK-N-SH	brain:	n/a	n/a
4	EP300	chr2:98950609-98951716	SK-N-SH	brain:	n/a	chr2:98950850-98950864
5	JUND	chr2:98950595-98951475	SK-N-SH	brain:	n/a	chr2:98950941-98950953 chr2:98950861-98950870
6	EP300	chr2:98950530-98951479	SK-N-SH	brain:	n/a	chr2:98950850-98950864
7	MAFK	chr2:98950568-98951160	IMR90	lung:	n/a	n/a
8	GATA3	chr2:98950635-98951843	SK-N-SH	brain:	n/a	chr2:98951498-98951514
9	EP300	chr2:98950639-98951816	SK-N-SH	brain:	n/a	chr2:98950850-98950864
10	FOXM1	chr2:98950490-98951664	SK-N-SH	brain:	n/a	n/a
11	PBX3	chr2:98950345-98951513	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COA5-2	chr2:98950386-98950843	NONHSAT072698

Variant related genes	Relation type
ENSG00000222000	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10172281	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10190679	0.98[ASN][1000 genomes]
rs10199476	0.87[CHB][hapmap]
rs10201994	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs10202618	0.84[AFR][1000 genomes]
rs10203437	0.84[AFR][1000 genomes]
rs10210685	0.98[ASN][1000 genomes]
rs11124096	0.87[CHB][hapmap]
rs11124107	0.82[CHB][hapmap]
rs11673807	0.82[CHB][hapmap]
rs11679920	0.82[CHB][hapmap]
rs11889349	0.87[CHB][hapmap]
rs11895654	0.87[CHB][hapmap]
rs12478763	0.82[CHB][hapmap]
rs12622324	0.82[CHB][hapmap]
rs12999985	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs13014142	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs13394706	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13408372	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13427344	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13428221	0.91[ASN][1000 genomes]
rs13432099	0.98[ASN][1000 genomes]
rs1451251	0.87[CHB][hapmap]
rs1466944	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1504679	0.82[AFR][1000 genomes]
rs17429208	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055591	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2102270	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2122756	0.87[CHB][hapmap]
rs2202387	0.82[CHB][hapmap]
rs2221416	0.87[CHB][hapmap];0.81[AFR][1000 genomes]
rs2292118	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2292119	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[YRI][hapmap]
rs3769755	0.80[CHB][hapmap]
rs4374424	0.87[CHB][hapmap]
rs4455212	0.85[CHB][hapmap]
rs4477970	0.87[CHB][hapmap]
rs4479470	0.82[CHB][hapmap]
rs4608580	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs4632400	0.87[CHB][hapmap]
rs4851123	0.84[AFR][1000 genomes]
rs4851935	0.82[CHB][hapmap]
rs4851951	0.85[CHB][hapmap]
rs4851955	0.82[AFR][1000 genomes]
rs4851959	0.83[EUR][1000 genomes]
rs4851960	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56320609	0.96[ASN][1000 genomes]
rs60924437	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62156263	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62156264	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6543419	0.87[CHB][hapmap]
rs6543459	0.84[AFR][1000 genomes]
rs66464436	0.83[EUR][1000 genomes]
rs6715989	0.87[CHB][hapmap]
rs6725543	0.87[CHB][hapmap]
rs6742930	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6747344	0.82[CHB][hapmap]
rs6747410	1.00[CHB][hapmap]
rs6754222	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72819909	0.98[ASN][1000 genomes]
rs7571001	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7571110	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7572757	0.84[AFR][1000 genomes]
rs7578802	0.82[CHB][hapmap]
rs7580008	1.00[ASN][1000 genomes]
rs7586663	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589018	0.83[EUR][1000 genomes]
rs7601049	0.82[CHB][hapmap]
rs7606220	0.87[CHB][hapmap]
rs937726	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008645	chr2:98915767-99010743	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1010466	chr2:98938886-98998109	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1013617	chr2:98943377-99004173	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98948400-98951400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:98948800-98952800	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:98949000-98953200	Enhancers	Brain Germinal Matrix	brain
4	chr2:98949200-98950800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:98949200-98952000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:98949400-98951200	Enhancers	NHDF-Ad	bronchial
7	chr2:98949400-98951600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr2:98949600-98951200	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:98949600-98952200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:98950000-98950800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:98950000-98950800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr2:98950000-98950800	Flanking Active TSS	Osteobl	bone
13	chr2:98950000-98951000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:98950000-98951000	Enhancers	Fetal Brain Female	brain
15	chr2:98950000-98951000	Enhancers	HSMMtube	muscle
16	chr2:98950000-98951200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr2:98950000-98951800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:98950000-98952000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:98950000-98952000	Enhancers	NHLF	lung
20	chr2:98950200-98950800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:98950200-98950800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:98950200-98950800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:98950200-98950800	Flanking Active TSS	HSMM	muscle
24	chr2:98950200-98950800	Flanking Active TSS	NH-A	brain
25	chr2:98950200-98951400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:98950200-98951600	Enhancers	A549	lung
27	chr2:98950200-98951600	Enhancers	HMEC	breast
28	chr2:98950200-98951600	Enhancers	NHEK	skin
29	chr2:98950200-98951800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:98950200-98951800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr2:98950200-98952000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:98950400-98950800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr2:98950400-98950800	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr2:98950400-98950800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:98950400-98950800	Enhancers	Brain Cingulate Gyrus	brain
36	chr2:98950400-98950800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr2:98950400-98951000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:98950400-98951000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:98950400-98951000	Enhancers	Fetal Brain Male	brain
40	chr2:98950400-98951400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:98950400-98951600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:98950400-98951600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:98950400-98951800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:98950600-98950800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:98950600-98951000	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr2:98950600-98951200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr2:98950600-98951400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:98950600-98951400	Enhancers	Colon Smooth Muscle	Colon
49	chr2:98950600-98951600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:98950600-98951600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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