Variant report

Variant	rs7996186
Chromosome Location	chr13:49107504-49107505
allele	C/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	ZBTB7A	chr13:49107264-49107533	K562	blood:	n/a	n/a
3	RELA	chr13:49104753-49107644	GM15510	blood:	n/a	n/a
4	POLR2A	chr13:49105879-49107776	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr13:49105471-49107535	GM12878	blood:	n/a	n/a
6	POLR2A	chr13:49105977-49107540	K562	blood:	n/a	n/a
7	POLR2A	chr13:49105070-49108079	GM15510	blood:	n/a	n/a
8	POLR2A	chr13:49106404-49107614	MCF-7	breast:	n/a	n/a
9	POLR2A	chr13:49104184-49108569	GM19099	blood:	n/a	n/a
10	POLR2A	chr13:49106447-49107820	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr13:49105884-49107692	Raji	blood:	n/a	n/a
12	POLR2A	chr13:49106409-49107614	MCF-7	breast:	n/a	n/a
13	TCF12	chr13:49106420-49107619	ECC-1	luminal epithelium:	n/a	n/a
14	POLR2A	chr13:49106520-49107617	A549	lung:	n/a	n/a
15	POLR2A	chr13:49106122-49107557	HL-60	blood:	n/a	n/a
16	POLR2A	chr13:49106443-49107544	U87	brain:	n/a	n/a
17	POLR2A	chr13:49106484-49107533	H1-neurons	neurons:	n/a	n/a
18	MTA3	chr13:49105442-49107850	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr13:49106376-49107590	MCF-7	breast:	n/a	n/a
20	POLR2A	chr13:49106013-49107789	ProgFib	skin:	n/a	n/a
21	HCFC1	chr13:49106021-49107892	Hela-S3	cervix:	n/a	n/a
22	CTCF	chr13:49107460-49107610	GM12873	blood:	n/a	n/a
23	MAZ	chr13:49106497-49107665	GM12878	blood:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
24	POLR2A	chr13:49106371-49107677	IMR90	lung:	n/a	n/a
25	POLR2A	chr13:49105979-49108447	PBDE	blood:	n/a	n/a
26	RELA	chr13:49105902-49107819	GM19099	blood:	n/a	n/a
27	POLR2A	chr13:49104358-49108010	GM18526	blood:	n/a	n/a
28	POLR2A	chr13:49106153-49107618	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr13:49106428-49107686	HEK293	kidney:	n/a	n/a
30	POLR2A	chr13:49104093-49108393	GM19193	blood:	n/a	n/a
31	POLR2A	chr13:49106270-49107609	HUVEC	blood vessel:	n/a	n/a
32	RELA	chr13:49104743-49107510	GM18951	blood:	n/a	n/a
33	POLR2A	chr13:49106399-49107542	HUVEC	blood vessel:	n/a	n/a
34	WRNIP1	chr13:49107159-49107769	GM12878	blood:	n/a	n/a
35	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
36	ELF1	chr13:49106380-49107599	GM12878	blood:	n/a	chr13:49106900-49106912 chr13:49107452-49107464
37	MAZ	chr13:49106053-49108571	IMR90	lung:	n/a	chr13:49106870-49106879 chr13:49107330-49107340
38	ZBTB7A	chr13:49106181-49107791	ECC-1	luminal epithelium:	n/a	chr13:49106785-49106794
39	POLR2A	chr13:49106068-49107999	NB4	blood:	n/a	n/a
40	POLR2A	chr13:49106468-49107594	Gliobla	brain:	n/a	n/a
41	ZBTB7A	chr13:49106371-49107815	ECC-1	luminal epithelium:	n/a	chr13:49106785-49106794
42	POLR2A	chr13:49102123-49108646	GM12891	blood:	n/a	n/a
43	POLR2A	chr13:49105737-49107568	HUVEC	blood vessel:	n/a	n/a
44	TAF1	chr13:49106209-49107586	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr13:49104148-49108484	GM18505	blood:	n/a	n/a
46	POLR2A	chr13:49105438-49107526	GM12892	blood:	n/a	n/a
47	SIN3A	chr13:49106411-49107564	H1-hESC	embryonic stem cell:	n/a	chr13:49107336-49107349
48	POLR2A	chr13:49106358-49107518	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr13:49106363-49107591	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr13:49104982-49107594	GM10847	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49107002..49107509-chr13:107220001..107220517,2	Hela-S3	cervix:
2	chr13:49106639..49107516-chr14:60714929..60715777,2	Hela-S3	cervix:

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

Variant related genes	Relation type
RCBTB2	TF binding region
ENSG00000134884	Chromatin interaction
ENSG00000254718	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1547660	0.91[ASN][1000 genomes]
rs174857	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs1926595	0.91[ASN][1000 genomes]
rs1926596	1.00[ASN][1000 genomes]
rs1926597	0.91[ASN][1000 genomes]
rs198568	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198571	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198574	0.89[JPT][hapmap]
rs198575	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198576	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198577	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs198606	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198609	0.86[CHB][hapmap]
rs198610	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198614	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs198622	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2274400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28414460	1.00[ASN][1000 genomes]
rs2854353	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2854357	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs2854362	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs28646083	1.00[ASN][1000 genomes]
rs28674973	0.93[ASN][1000 genomes]
rs3092888	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs3092899	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs3751380	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs398158	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs403390	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs406098	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs4151448	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs4151452	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs4151456	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4151461	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4151474	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap]
rs4151525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4151601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs425834	0.88[CHB][hapmap]
rs427686	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs56871512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58001261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58854758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58933677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60887299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61074776	0.91[ASN][1000 genomes]
rs6561448	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6561457	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6561461	0.85[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7325962	0.90[JPT][hapmap]
rs7329039	0.91[ASN][1000 genomes]
rs7329865	1.00[CEU][hapmap]
rs7331851	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs73486867	0.91[ASN][1000 genomes]
rs7981869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7985825	0.91[ASN][1000 genomes]
rs7987935	1.00[ASN][1000 genomes]
rs7989969	1.00[AFR][1000 genomes]
rs7992129	0.91[ASN][1000 genomes]
rs7995216	1.00[CEU][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7996402	0.91[ASN][1000 genomes]
rs7998781	0.88[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8001241	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs8002565	0.88[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9316385	0.90[ASN][1000 genomes]
rs9316401	0.91[ASN][1000 genomes]
rs9331959	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9331965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9331973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9332054	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9591172	0.91[ASN][1000 genomes]
rs9591177	0.90[ASN][1000 genomes]
rs9591178	0.91[ASN][1000 genomes]

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:126 , 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	chr13:49105600-49107600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:49105600-49107600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:49105600-49107800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
5	chr13:49105600-49107800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr13:49105800-49107600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr13:49105800-49107600	Active TSS	Fetal Intestine Small	intestine
8	chr13:49105800-49107600	Active TSS	Left Ventricle	heart
9	chr13:49105800-49107600	Active TSS	Ovary	ovary
10	chr13:49105800-49107600	Active TSS	Pancreas	Pancrea
11	chr13:49105800-49107600	Active TSS	HSMM	muscle
12	chr13:49105800-49107800	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr13:49105800-49107800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr13:49105800-49107800	Active TSS	Aorta	Aorta
15	chr13:49105800-49107800	Active TSS	Duodenum Mucosa	Duodenum
16	chr13:49105800-49107800	Active TSS	Fetal Kidney	kidney
17	chr13:49105800-49107800	Active TSS	A549	lung
18	chr13:49105800-49108000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr13:49106000-49107600	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr13:49106000-49107600	Active TSS	Colon Smooth Muscle	Colon
21	chr13:49106000-49107600	Active TSS	Esophagus	oesophagus
22	chr13:49106000-49107600	Active TSS	Small Intestine	intestine
23	chr13:49106000-49107800	Active TSS	Right Ventricle	heart
24	chr13:49106000-49108000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr13:49106000-49108000	Active TSS	H9 Cell Line	embryonic stem cell
26	chr13:49106200-49107600	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr13:49106200-49107600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:49106200-49107600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:49106200-49107600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:49106200-49107600	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr13:49106200-49107600	Active TSS	Liver	Liver
32	chr13:49106200-49107600	Active TSS	Brain Anterior Caudate	brain
33	chr13:49106200-49107600	Active TSS	Brain Cingulate Gyrus	brain
34	chr13:49106200-49107600	Active TSS	Brain Germinal Matrix	brain
35	chr13:49106200-49107600	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr13:49106200-49107600	Active TSS	Brain Substantia Nigra	brain
37	chr13:49106200-49107600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr13:49106200-49107600	Active TSS	Fetal Heart	heart
39	chr13:49106200-49107600	Active TSS	Fetal Lung	lung
40	chr13:49106200-49107600	Active TSS	Fetal Stomach	stomach
41	chr13:49106200-49107600	Active TSS	Placenta Amnion	Placenta Amnion
42	chr13:49106200-49107600	Active TSS	Rectal Smooth Muscle	rectum
43	chr13:49106200-49107600	Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr13:49106200-49107600	Active TSS	HSMMtube	muscle
45	chr13:49106200-49107600	Active TSS	NH-A	brain
46	chr13:49106200-49107600	Active TSS	NHEK	skin
47	chr13:49106200-49107600	Active TSS	NHLF	lung
48	chr13:49106200-49107800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr13:49106200-49107800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr13:49106200-49107800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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