Variant report

Variant	rs8001241
Chromosome Location	chr13:49107653-49107654
allele	A/G
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	chr13:49105321-49107960	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:49105879-49107776	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr13:49105070-49108079	GM15510	blood:	n/a	n/a
4	POLR2A	chr13:49104184-49108569	GM19099	blood:	n/a	n/a
5	POLR2A	chr13:49106447-49107820	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr13:49105884-49107692	Raji	blood:	n/a	n/a
7	CTCF	chr13:49107560-49107710	GM12872	blood:	n/a	n/a
8	MTA3	chr13:49105442-49107850	GM12878	blood:	n/a	n/a
9	POLR2A	chr13:49106013-49107789	ProgFib	skin:	n/a	n/a
10	HCFC1	chr13:49106021-49107892	Hela-S3	cervix:	n/a	n/a
11	MAZ	chr13:49106497-49107665	GM12878	blood:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
12	POLR2A	chr13:49106371-49107677	IMR90	lung:	n/a	n/a
13	POLR2A	chr13:49105979-49108447	PBDE	blood:	n/a	n/a
14	RELA	chr13:49105902-49107819	GM19099	blood:	n/a	n/a
15	POLR2A	chr13:49104358-49108010	GM18526	blood:	n/a	n/a
16	POLR2A	chr13:49106428-49107686	HEK293	kidney:	n/a	n/a
17	POLR2A	chr13:49104093-49108393	GM19193	blood:	n/a	n/a
18	WRNIP1	chr13:49107159-49107769	GM12878	blood:	n/a	n/a
19	NRF1	chr13:49105990-49107897	SK-N-SH	brain:	n/a	chr13:49106806-49106817 chr13:49106808-49106817 chr13:49106885-49106899 chr13:49106968-49106982 chr13:49106887-49106898 chr13:49106806-49106815 chr13:49106803-49106817 chr13:49106973-49106982 chr13:49106888-49106897 chr13:49106888-49106899 chr13:49106971-49106982 chr13:49106890-49106899 chr13:49106806-49106820 chr13:49106971-49106985 chr13:49106888-49106902
20	MAZ	chr13:49106053-49108571	IMR90	lung:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
21	ZBTB7A	chr13:49106181-49107791	ECC-1	luminal epithelium:	n/a	chr13:49106785-49106794
22	POLR2A	chr13:49106068-49107999	NB4	blood:	n/a	n/a
23	ZBTB7A	chr13:49106371-49107815	ECC-1	luminal epithelium:	n/a	chr13:49106785-49106794
24	POLR2A	chr13:49102123-49108646	GM12891	blood:	n/a	n/a
25	CHD1	chr13:49107652-49107719	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr13:49104148-49108484	GM18505	blood:	n/a	n/a
27	POLR2A	chr13:49103707-49108625	GM12878	blood:	n/a	n/a
28	REST	chr13:49106224-49107946	H1-neurons	neurons:	n/a	n/a
29	MAX	chr13:49106543-49107664	NB4	blood:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
30	POLR2A	chr13:49106421-49107723	GM12878	blood:	n/a	n/a
31	POLR2A	chr13:49104171-49108266	GM18951	blood:	n/a	n/a
32	POLR2A	chr13:49107488-49107783	GM12891	blood:	n/a	n/a
33	POLR2A	chr13:49106041-49107935	MCF10A-Er-Src	breast:	n/a	n/a
34	ZNF143	chr13:49106573-49107731	GM12878	blood:	n/a	chr13:49107057-49107075
35	POLR2A	chr13:49104669-49108203	GM12892	blood:	n/a	n/a
36	USF2	chr13:49107615-49107738	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49107619..49110446-chr13:49111219..49113821,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RB1-2	chr13:49106976-49107897	NONHSAT033718

Variant related genes	Relation type
RCBTB2	TF binding region

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1547660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174857	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs1926595	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926596	0.91[ASN][1000 genomes]
rs1926597	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198564	0.85[ASN][1000 genomes]
rs198568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198571	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs198574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.88[ASN][1000 genomes]
rs198575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs198606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs198609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs198610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198614	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs198622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2274400	0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs28414460	0.91[ASN][1000 genomes]
rs2854353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2854362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28646083	0.91[ASN][1000 genomes]
rs28674973	0.84[ASN][1000 genomes]
rs2897587	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs3092888	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3092898	0.88[ASN][1000 genomes]
rs3092899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3751380	0.87[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs398158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs403390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs406098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs4151448	1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap]
rs4151452	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4151456	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4151474	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4151525	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4151601	0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap]
rs425834	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs427686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs449268	0.91[MEX][hapmap];0.87[TSI][hapmap]
rs61074776	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561461	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561465	1.00[CEU][hapmap]
rs7325962	1.00[ASW][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7326934	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7329039	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7329865	0.88[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs73486867	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73495016	0.88[ASN][1000 genomes]
rs7985825	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987935	0.91[ASN][1000 genomes]
rs7992129	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995216	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7996186	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7996402	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8002565	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];1.00[ASN][1000 genomes]
rs9316385	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316386	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs9316396	1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9316401	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331959	0.91[ASN][1000 genomes]
rs9331965	0.88[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs9331973	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9332054	0.94[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs9591172	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9591177	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591178	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9595929	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9595931	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49105400-49107800	Active TSS	Right Atrium	heart
2	chr13:49105600-49107800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
3	chr13:49105600-49107800	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr13:49105800-49107800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr13:49105800-49107800	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:49105800-49107800	Active TSS	Aorta	Aorta
7	chr13:49105800-49107800	Active TSS	Duodenum Mucosa	Duodenum
8	chr13:49105800-49107800	Active TSS	Fetal Kidney	kidney
9	chr13:49105800-49107800	Active TSS	A549	lung
10	chr13:49105800-49108000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr13:49106000-49107800	Active TSS	Right Ventricle	heart
12	chr13:49106000-49108000	Active TSS	H1 Cell Line	embryonic stem cell
13	chr13:49106000-49108000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr13:49106200-49107800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr13:49106200-49107800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:49106200-49107800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr13:49106200-49107800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr13:49106200-49107800	Active TSS	Fetal Brain Female	brain
19	chr13:49106200-49108000	Active TSS	K562	blood
20	chr13:49106200-49108400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr13:49106400-49107800	Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr13:49107000-49107800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr13:49107200-49107800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr13:49107200-49107800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr13:49107200-49107800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr13:49107200-49107800	Flanking Active TSS	Colonic Mucosa	Colon
27	chr13:49107200-49108000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:49107200-49108200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr13:49107200-49108200	Flanking Active TSS	GM12878-XiMat	blood
30	chr13:49107200-49108600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr13:49107200-49110800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr13:49107400-49107800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr13:49107400-49107800	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr13:49107400-49107800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:49107400-49107800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr13:49107400-49107800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr13:49107400-49107800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr13:49107400-49107800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr13:49107400-49107800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:49107400-49107800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr13:49107400-49107800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:49107400-49107800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr13:49107400-49107800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:49107400-49107800	Flanking Active TSS	Brain Angular Gyrus	brain
45	chr13:49107400-49107800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr13:49107400-49107800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr13:49107400-49107800	Flanking Active TSS	Fetal Intestine Large	intestine
48	chr13:49107400-49107800	Flanking Active TSS	Fetal Muscle Trunk	muscle
49	chr13:49107400-49107800	Flanking Active TSS	Placenta	Placenta
50	chr13:49107400-49107800	Flanking Active TSS	Fetal Thymus	thymus

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