Variant report

Variant	rs10836397
Chromosome Location	chr11:4658068-4658069
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	MAX	chr11:4658049-4658545	H1-hESC	embryonic stem cell:	n/a	n/a
2	RAD21	chr11:4658037-4658479	MCF-7	breast:	n/a	chr11:4658299-4658318
3	MAX	chr11:4658054-4658586	H1-hESC	embryonic stem cell:	n/a	n/a
4	RAD21	chr11:4658062-4658730	H1-hESC	embryonic stem cell:	n/a	chr11:4658299-4658318
5	CTCF	chr11:4658041-4658500	MCF-7	breast:	n/a	chr11:4658301-4658314 chr11:4658486-4658494 chr11:4658299-4658315 chr11:4658300-4658321 chr11:4658298-4658316 chr11:4658423-4658431
6	RAD21	chr11:4658035-4658614	HCT-116	colon:	n/a	chr11:4658299-4658318
7	RAD21	chr11:4658010-4658582	H1-hESC	embryonic stem cell:	n/a	chr11:4658299-4658318
8	RAD21	chr11:4658043-4658691	HCT-116	colon:	n/a	chr11:4658299-4658318
9	RAD21	chr11:4658067-4658557	SK-N-SH_RA	brain:	n/a	chr11:4658299-4658318
10	CTCF	chr11:4657925-4658636	A549	lung:	n/a	chr11:4658301-4658314 chr11:4658486-4658494 chr11:4658299-4658315 chr11:4658300-4658321 chr11:4658298-4658316 chr11:4658423-4658431
11	RAD21	chr11:4658042-4658605	ECC-1	luminal epithelium:	n/a	chr11:4658299-4658318
12	RAD21	chr11:4658065-4658546	ECC-1	luminal epithelium:	n/a	chr11:4658299-4658318
13	RAD21	chr11:4658025-4658528	HepG2	liver:	n/a	chr11:4658299-4658318
14	RAD21	chr11:4658027-4658624	A549	lung:	n/a	chr11:4658299-4658318
15	SMC3	chr11:4657857-4658620	SK-N-SH	brain:	n/a	chr11:4658300-4658314
16	RAD21	chr11:4658057-4658738	IMR90	lung:	n/a	chr11:4658299-4658318
17	CTCF	chr11:4658063-4658495	H1-hESC	embryonic stem cell:	n/a	chr11:4658301-4658314 chr11:4658486-4658494 chr11:4658299-4658315 chr11:4658300-4658321 chr11:4658298-4658316 chr11:4658423-4658431
18	RAD21	chr11:4658037-4658543	H1-hESC	embryonic stem cell:	n/a	chr11:4658299-4658318
19	RAD21	chr11:4657905-4658740	SK-N-SH	brain:	n/a	chr11:4658299-4658318
20	CTCF	chr11:4657881-4658648	SK-N-SH	brain:	n/a	chr11:4658301-4658314 chr11:4658486-4658494 chr11:4658299-4658315 chr11:4658300-4658321 chr11:4658298-4658316 chr11:4658423-4658431
21	RAD21	chr11:4658014-4658553	MCF-7	breast:	n/a	chr11:4658299-4658318

No.	Distal block	Cell Line	Cell type
1	chr11:4657777..4658387-chr11:5025582..5026377,4	MCF-7	breast:
2	chr11:4657777..4658777-chr11:5012019..5012933,4	K562	blood:
3	chr11:4657872..4658731-chr11:5025387..5026540,3	K562	blood:
4	chr11:4657833..4658473-chr11:4847439..4848013,2	MCF-7	breast:
5	chr11:4658042..4658694-chr11:4667228..4668066,2	K562	blood:
6	chr11:4657985..4658755-chr11:5391194..5391750,2	MCF-7	breast:

Variant related genes	Relation type
OR51D1	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10836399	0.95[JPT][hapmap]
rs11033126	0.95[JPT][hapmap]
rs12293250	0.81[ASN][1000 genomes]
rs12787640	0.86[JPT][hapmap]
rs1983100	0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1983101	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2412391	0.81[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	nsv1043803	chr11:4388448-4837042	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv540916	chr11:4388448-4837042	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats 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	46 gene(s)	inside rSNPs	diseases
3	nsv1048224	chr11:4390227-4920324	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
4	nsv540917	chr11:4390227-4920324	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
5	nsv896911	chr11:4400801-4806872	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv832055	chr11:4550894-4736340	Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1054705	chr11:4582150-4687238	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	esv3424302	chr11:4585155-4880050	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv553173	chr11:4587940-4689742	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1054801	chr11:4590126-4689520	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv540923	chr11:4590126-4689520	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv553174	chr11:4592718-4682376	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv1041836	chr11:4594628-4685732	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv540924	chr11:4594628-4685732	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1047741	chr11:4598125-4689520	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv540925	chr11:4598125-4689520	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv540929	chr11:4628274-4669343	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv540931	chr11:4631455-4662608	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv540932	chr11:4631455-4666157	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	nsv540933	chr11:4633452-4662548	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv540934	chr11:4633452-4662608	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv540935	chr11:4633452-4666157	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv540936	chr11:4633452-4669343	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv1041633	chr11:4639292-4693109	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv1054847	chr11:4642875-5200656	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10836397	OR52N1	cis	parietal	SCAN
rs10836397	SLC25A22	cis	parietal	SCAN
rs10836397	H19	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:4658000-4658200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr11:4658000-4658200	Bivalent Enhancer	Brain Cingulate Gyrus	brain
3	chr11:4658000-4658200	Enhancers	Brain Inferior Temporal Lobe	brain
4	chr11:4658000-4658200	Enhancers	Brain Substantia Nigra	brain
5	chr11:4658000-4658200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
6	chr11:4658000-4658200	Flanking Active TSS	Ovary	ovary
7	chr11:4658000-4658200	Weak transcription	Right Atrium	heart
8	chr11:4658000-4658200	Flanking Bivalent TSS/Enh	K562	blood
9	chr11:4658000-4658400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr11:4658000-4658400	Enhancers	Right Ventricle	heart
11	chr11:4658000-4658600	Enhancers	Primary B cells from peripheral blood	blood
12	chr11:4658000-4658600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:4658000-4658600	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr11:4658000-4658600	Active TSS	Stomach Smooth Muscle	stomach
15	chr11:4658000-4658800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:4658000-4658800	Flanking Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links