Variant report

Variant	rs13327031
Chromosome Location	chr3:113251935-113251936
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	ELF1	chr3:113251530-113252455	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:113250612-113252829	GM12878	blood:	n/a	n/a
3	MAX	chr3:113251083-113252569	A549	lung:	n/a	n/a
4	POLR2A	chr3:113250679-113252858	GM12892	blood:	n/a	n/a
5	CTCF	chr3:113251900-113252050	GM12871	blood:	n/a	n/a
6	POLR2A	chr3:113250651-113251955	GM12892	blood:	n/a	n/a
7	MXI1	chr3:113250820-113253859	GM12878	blood:	n/a	chr3:113253277-113253292 chr3:113253275-113253290
8	RUNX3	chr3:113250656-113251948	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:113250783-113252763	GM18526	blood:	n/a	n/a
10	EBF1	chr3:113251162-113252765	GM12878	blood:	n/a	chr3:113252160-113252173 chr3:113252162-113252171 chr3:113252160-113252171 chr3:113252161-113252171
11	POLR2A	chr3:113250736-113252819	GM19099	blood:	n/a	n/a
12	POLR2A	chr3:113250694-113252114	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:113250676-113253816	GM12878	blood:	n/a	n/a
14	ELF1	chr3:113250787-113252010	GM12878	blood:	n/a	chr3:113251073-113251082 chr3:113251072-113251083
15	POLR2A	chr3:113251227-113252715	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:113250676-113252838	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:113251585-113252059	MCF-7	breast:	n/a	n/a
18	POLR2A	chr3:113251852-113252125	ProgFib	skin:	n/a	n/a
19	YY1	chr3:113251223-113252045	GM12892	blood:	n/a	n/a
20	MAX	chr3:113251563-113252480	H1-hESC	embryonic stem cell:	n/a	n/a
21	PML	chr3:113250515-113253049	GM12878	blood:	n/a	chr3:113250961-113250969
22	CTCF	chr3:113251820-113251970	HMEC	breast:	n/a	n/a
23	EBF1	chr3:113250940-113254059	GM12878	blood:	n/a	chr3:113252160-113252173 chr3:113252162-113252171 chr3:113252160-113252171 chr3:113253045-113253055 chr3:113252161-113252171
24	POLR2A	chr3:113250808-113252783	GM18951	blood:	n/a	n/a
25	CHD1	chr3:113250775-113252916	GM12878	blood:	n/a	chr3:113252282-113252292
26	RELA	chr3:113250879-113252782	GM15510	blood:	n/a	n/a
27	POLR2A	chr3:113250831-113252757	Raji	blood:	n/a	n/a
28	MAX	chr3:113251787-113251988	HepG2	liver:	n/a	n/a
29	STAT1	chr3:113251904-113252752	GM12878	blood:	n/a	chr3:113252233-113252245
30	MAX	chr3:113250979-113252787	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:113250654-113253857	GM12891	blood:	n/a	n/a
32	SIN3AK20	chr3:113250966-113253849	MCF-7	breast:	n/a	n/a
33	STAT5A	chr3:113250700-113252153	GM12878	blood:	n/a	chr3:113251366-113251377
34	E2F6	chr3:113251586-113252498	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr3:113251915-113253914	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:113250707-113252818	GM15510	blood:	n/a	n/a
37	POLR2A	chr3:113251194-113252720	GM10847	blood:	n/a	n/a
38	PAX5	chr3:113251516-113252039	GM12892	blood:	n/a	n/a
39	TCF7L2	chr3:113251729-113252000	PANC-1	pancreas:	n/a	n/a
40	ZNF143	chr3:113251733-113252365	GM12878	blood:	n/a	n/a
41	YY1	chr3:113251681-113252734	GM12878	blood:	n/a	n/a
42	CTCF	chr3:113251800-113251950	GM12869	blood:	n/a	n/a
43	POLR2A	chr3:113250648-113253918	GM12878	blood:	n/a	n/a
44	SUZ12	chr3:113251261-113252608	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr3:113250767-113252753	GM19193	blood:	n/a	n/a
46	CHD2	chr3:113251015-113252826	GM12878	blood:	n/a	chr3:113252282-113252292
47	CTCF	chr3:113251800-113251950	NHEK	skin:	n/a	n/a
48	CTCF	chr3:113251860-113252010	GM12870	blood:	n/a	n/a
49	POLR2A	chr3:113251148-113252397	H1-neurons	neurons:	n/a	n/a
50	ZBTB7A	chr3:113251500-113252232	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:113250521..113252326-chr3:113465017..113467077,2	MCF-7	breast:
2	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
3	chr20:61846286..61848363-chr3:113251582..113253331,2	MCF-7	breast:

Variant related genes	Relation type
SIDT1	TF binding region
ENSG00000149658	Chromatin interaction
ENSG00000114573	Chromatin interaction
ENSG00000163611	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000121579	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs13326562	0.90[EUR][1000 genomes]
rs13353449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2399487	1.00[EUR][1000 genomes]
rs28539944	0.81[EUR][1000 genomes]
rs28614095	0.81[EUR][1000 genomes]
rs4419353	1.00[EUR][1000 genomes]
rs6438154	1.00[EUR][1000 genomes]
rs6763234	1.00[EUR][1000 genomes]
rs6779241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6780720	1.00[EUR][1000 genomes]
rs6781507	1.00[EUR][1000 genomes]
rs6797630	0.81[EUR][1000 genomes]
rs6808103	1.00[EUR][1000 genomes]
rs72950895	0.81[EUR][1000 genomes]
rs7612448	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7618195	0.86[EUR][1000 genomes]
rs7625829	0.95[EUR][1000 genomes]
rs7629636	1.00[EUR][1000 genomes]
rs7645188	1.00[EUR][1000 genomes]
rs9810059	1.00[EUR][1000 genomes]
rs9810754	0.81[EUR][1000 genomes]
rs9811168	0.90[EUR][1000 genomes]
rs9827490	0.81[EUR][1000 genomes]
rs9827772	0.86[EUR][1000 genomes]
rs9836199	0.90[EUR][1000 genomes]
rs9846529	0.81[EUR][1000 genomes]
rs9851183	0.90[EUR][1000 genomes]
rs9851407	0.95[EUR][1000 genomes]
rs9852068	1.00[EUR][1000 genomes]
rs9860473	0.95[EUR][1000 genomes]
rs9878186	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS 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	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113250400-113252800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr3:113250400-113253200	Active TSS	Sigmoid Colon	Sigmoid Colon
3	chr3:113250600-113253200	Active TSS	Thymus	Thymus
4	chr3:113250600-113253400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:113250800-113252000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
6	chr3:113250800-113252200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr3:113250800-113252400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr3:113250800-113253000	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:113250800-113253000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
10	chr3:113250800-113253000	Bivalent/Poised TSS	A549	lung
11	chr3:113250800-113253200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:113250800-113253200	Active TSS	Rectal Smooth Muscle	rectum
13	chr3:113250800-113253200	Active TSS	Stomach Mucosa	stomach
14	chr3:113250800-113254600	Active TSS	GM12878-XiMat	blood
15	chr3:113251000-113252000	Active TSS	Primary hematopoietic stem cells	blood
16	chr3:113251000-113252200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:113251000-113252200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:113251000-113252200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:113251000-113252200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr3:113251000-113252200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr3:113251000-113252200	Active TSS	Right Ventricle	heart
22	chr3:113251000-113252200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
23	chr3:113251000-113252400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr3:113251000-113252400	Active TSS	Primary B cells from peripheral blood	blood
25	chr3:113251000-113252400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr3:113251000-113252400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr3:113251000-113252400	Active TSS	Brain Angular Gyrus	brain
28	chr3:113251000-113252400	Active TSS	Fetal Thymus	thymus
29	chr3:113251000-113252400	Active TSS	Right Atrium	heart
30	chr3:113251000-113252400	Bivalent/Poised TSS	NHDF-Ad	bronchial
31	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
32	chr3:113251000-113252600	Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr3:113251000-113252600	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr3:113251000-113252600	Flanking Active TSS	Liver	Liver
35	chr3:113251000-113252600	Active TSS	Brain Substantia Nigra	brain
36	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
37	chr3:113251000-113252600	Active TSS	Small Intestine	intestine
38	chr3:113251000-113252600	Flanking Bivalent TSS/Enh	NHEK	skin
39	chr3:113251000-113252800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr3:113251000-113252800	Active TSS	Primary T cells fromperipheralblood	blood
41	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:113251000-113252800	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr3:113251000-113252800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:113251000-113252800	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr3:113251000-113252800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
46	chr3:113251000-113252800	Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr3:113251000-113253200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr3:113251000-113253200	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr3:113251000-113253800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:113251200-113252000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links