Variant report

Variant	rs2237116
Chromosome Location	chr6:15499050-15499051
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	chr6:15498853-15499114	GM12878	blood:	n/a	n/a
2	MAX	chr6:15498868-15499196	K562	blood:	n/a	chr6:15498998-15499013 chr6:15498999-15499010
3	E2F4	chr6:15499006-15499206	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr6:15498756-15499196	GM12891	blood:	n/a	n/a
5	FOS	chr6:15498906-15499242	MCF10A-Er-Src	breast:	n/a	chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105
6	POLR2A	chr6:15498482-15499657	H1-hESC	embryonic stem cell:	n/a	n/a
7	FOS	chr6:15498894-15499213	MCF10A-Er-Src	breast:	n/a	chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105
8	POLR2A	chr6:15498609-15499458	Hela-S3	cervix:	n/a	n/a
9	MAX	chr6:15498877-15499083	K562	blood:	n/a	chr6:15498998-15499013 chr6:15498999-15499010
10	POLR2A	chr6:15498831-15499149	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:15498501-15499663	H1-hESC	embryonic stem cell:	n/a	n/a
12	STAT3	chr6:15498922-15499099	MCF10A-Er-Src	breast:	n/a	chr6:15498988-15498999
13	BHLHE40	chr6:15498839-15499194	K562	blood:	n/a	chr6:15499000-15499009 chr6:15498915-15498931 chr6:15499000-15499009
14	POLR2A	chr6:15498520-15500203	H1-hESC	embryonic stem cell:	n/a	n/a
15	STAT3	chr6:15498916-15499116	MCF10A-Er-Src	breast:	n/a	chr6:15498988-15498999
16	MYC	chr6:15499013-15499077	MCF-7	breast:	n/a	n/a
17	MYC	chr6:15498877-15499209	MCF10A-Er-Src	breast:	n/a	chr6:15498998-15499013 chr6:15498999-15499010
18	POLR2A	chr6:15498579-15500253	GM12878	blood:	n/a	n/a
19	FOS	chr6:15498920-15499231	MCF10A-Er-Src	breast:	n/a	chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105
20	POLR2A	chr6:15499010-15499303	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr6:15498346-15500236	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr6:15498987-15499238	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:15498517-15499398	GM12878	blood:	n/a	n/a
24	STAT3	chr6:15498931-15499160	MCF10A-Er-Src	breast:	n/a	chr6:15498988-15498999
25	MYC	chr6:15498877-15499220	MCF10A-Er-Src	breast:	n/a	chr6:15498998-15499013 chr6:15498999-15499010
26	POLR2A	chr6:15498071-15500211	K562	blood:	n/a	n/a
27	FOS	chr6:15498908-15499222	MCF10A-Er-Src	breast:	n/a	chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105 chr6:15499095-15499105

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15497600..15499927-chr6:15509005..15511322,2	K562	blood:

Variant related genes	Relation type
JARID2	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2072821	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2072822	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs2237113	0.82[CHB][hapmap]
rs2237120	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237123	0.82[CHB][hapmap]
rs2237124	0.81[CHB][hapmap]
rs2237139	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs2282819	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299045	0.80[CHB][hapmap]
rs2299059	0.94[CEU][hapmap]
rs3800496	0.86[CHB][hapmap]
rs3800497	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56259001	0.85[EUR][1000 genomes]
rs742101	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9396588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396589	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9396590	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9396591	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv522265	chr6:15494177-15546213	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15471000-15502000	Weak transcription	A549	lung
2	chr6:15486800-15502000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:15487200-15508000	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr6:15489200-15504400	Weak transcription	Fetal Brain Female	brain
5	chr6:15491800-15501400	Weak transcription	NH-A	brain
6	chr6:15492000-15501800	Weak transcription	Fetal Brain Male	brain
7	chr6:15492200-15501200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:15492200-15507800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:15492200-15508200	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr6:15492200-15527000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:15492400-15502400	Strong transcription	Fetal Intestine Small	intestine
12	chr6:15492400-15527200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:15492600-15522200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:15492800-15515000	Strong transcription	Thymus	Thymus
15	chr6:15492800-15527000	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:15493000-15501600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr6:15493000-15501600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr6:15493000-15501800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:15493000-15504200	Strong transcription	Fetal Thymus	thymus
20	chr6:15493400-15502000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr6:15493800-15520000	Weak transcription	Hela-S3	cervix
22	chr6:15494200-15522400	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr6:15494400-15501600	Weak transcription	Fetal Kidney	kidney
24	chr6:15494600-15506000	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr6:15494600-15507400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:15494800-15524000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:15494800-15527000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr6:15495000-15499200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:15495000-15499800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:15495000-15527200	Strong transcription	Dnd41	blood
31	chr6:15495000-15529200	Strong transcription	Primary T cells from cord blood	blood
32	chr6:15495200-15508400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:15495200-15525800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr6:15495400-15504200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:15495400-15504800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:15495400-15506400	Strong transcription	H9 Cell Line	embryonic stem cell
37	chr6:15495400-15508600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr6:15495400-15525000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:15495600-15502000	Weak transcription	Psoas Muscle	Psoas
40	chr6:15495600-15503200	Strong transcription	HepG2	liver
41	chr6:15495600-15504200	Weak transcription	NHDF-Ad	bronchial
42	chr6:15495800-15500000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:15495800-15501800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr6:15495800-15503000	Strong transcription	Liver	Liver
45	chr6:15495800-15505800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr6:15495800-15506800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr6:15496000-15499400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:15496000-15507000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:15496000-15525200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr6:15496000-15525600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links