Variant report

Variant	rs11771139
Chromosome Location	chr7:99736059-99736060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99735365..99737533-chr7:99748809..99751456,2	MCF-7	breast:
2	chr7:99735959..99737658-chr7:99745267..99748178,2	MCF-7	breast:
3	chr7:99735323..99737033-chr7:99747099..99749402,2	K562	blood:
4	chr7:99734202..99739266-chr7:99744673..99748688,7	MCF-7	breast:
5	chr4:75240541..75242420-chr7:99735391..99737908,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188186	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10281368	0.84[ASW][hapmap];0.83[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap]
rs1043915	0.83[CEU][hapmap]
rs1061230	0.83[CEU][hapmap]
rs11505847	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11764176	0.83[CEU][hapmap]
rs12666425	0.83[CEU][hapmap]
rs12705070	0.83[CHB][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs12705071	0.93[TSI][hapmap]
rs13223792	0.83[CHB][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap]
rs13230744	0.81[CEU][hapmap]
rs1527423	0.91[YRI][hapmap]
rs1623264	0.82[CEU][hapmap]
rs1636975	0.83[CEU][hapmap]
rs1637001	0.83[CEU][hapmap]
rs1727133	0.83[CEU][hapmap]
rs1727134	0.83[CEU][hapmap]
rs1727138	0.83[CEU][hapmap]
rs1727140	0.83[CEU][hapmap]
rs1880949	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[GIH][hapmap];0.80[JPT][hapmap];0.91[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2070215	0.94[TSI][hapmap]
rs2141160	0.81[CEU][hapmap]
rs2272345	0.83[CEU][hapmap]
rs2293479	0.82[CEU][hapmap];0.91[YRI][hapmap]
rs2528900	0.83[CEU][hapmap]
rs2950520	0.82[ASW][hapmap];0.83[CEU][hapmap]
rs34130487	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35146811	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35991721	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3779045	0.83[CEU][hapmap]
rs4134903	0.84[ASW][hapmap];0.82[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs4424195	0.83[CHB][hapmap];0.93[GIH][hapmap];0.94[TSI][hapmap]
rs6948729	0.83[CEU][hapmap]
rs7794170	0.82[CEU][hapmap]
rs7811662	0.83[CEU][hapmap]
rs858506	0.82[CEU][hapmap]
rs866500	0.83[CEU][hapmap]
rs999885	0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats 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 miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong 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 miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
9	nsv966865	chr7:99735585-99740478	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11771139	ZNF498	cis	cerebellum	SCAN
rs11771139	BUD31	cis	parietal	SCAN
rs11771139	PILRB	cis	parietal	SCAN
rs11771139	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs11771139	ZSCAN21	cis	parietal	SCAN
rs11771139	GATS	cis	multi-tissue	Pritchard
rs11771139	GAL3ST4	cis	cerebellum	SCAN
rs11771139	TRIM4	cis	multi-tissue	Pritchard
rs11771139	GATS	cis	parietal	SCAN
rs11771139	ZKSCAN1	cis	cerebellum	SCAN
rs11771139	PILRB	cis	multi-tissue	Pritchard
rs11771139	LRWD1	cis	parietal	SCAN
rs11771139	SHFM1	cis	parietal	SCAN
rs11771139	GATS	cis	cerebellum	SCAN
rs11771139	GATS	cis	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99728800-99740000	Weak transcription	Colonic Mucosa	Colon
2	chr7:99728800-99746000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:99730600-99738600	Weak transcription	Hela-S3	cervix
4	chr7:99731000-99745600	Weak transcription	Pancreas	Pancrea
5	chr7:99735200-99736400	Enhancers	Fetal Thymus	thymus
6	chr7:99735400-99736200	Enhancers	Primary T cells from cord blood	blood
7	chr7:99735400-99736200	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:99735400-99736200	Enhancers	Placenta	Placenta
9	chr7:99735400-99736200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr7:99735400-99736400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr7:99735400-99736400	Enhancers	Duodenum Mucosa	Duodenum
12	chr7:99735400-99736600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr7:99735400-99736800	Enhancers	Primary B cells from peripheral blood	blood
14	chr7:99735600-99736200	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr7:99735600-99736200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr7:99735600-99736200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr7:99735600-99736200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:99735600-99736200	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr7:99735600-99736200	Enhancers	Thymus	Thymus
20	chr7:99735600-99736400	Enhancers	Primary T cells fromperipheralblood	blood
21	chr7:99735600-99736400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr7:99735600-99736400	Enhancers	Stomach Mucosa	stomach
23	chr7:99735800-99736200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr7:99735800-99736200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr7:99736000-99736200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:99736000-99736200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:99736000-99736200	Enhancers	NHEK	skin
28	chr7:99736000-99736400	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr7:99736000-99736400	Enhancers	Fetal Intestine Small	intestine
30	chr7:99736000-99736400	Enhancers	GM12878-XiMat	blood
31	chr7:99736000-99739000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links