Variant report

Variant	rs7873862
Chromosome Location	chr9:116113396-116113397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116112976..116115054-chr9:116115085..116116590,2	K562	blood:
2	chr9:116110213..116113414-chr9:116171126..116174421,5	MCF-7	breast:
3	chr9:116111218..116114895-chr9:116159419..116161993,4	MCF-7	breast:
4	chr9:116108846..116117047-chr9:116126327..116140994,30	MCF-7	breast:
5	chr9:116064341..116066340-chr9:116112890..116114415,2	MCF-7	breast:
6	chr9:116035712..116039392-chr9:116113201..116116002,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119431	Chromatin interaction
ENSG00000148218	Chromatin interaction
ENSG00000165188	Chromatin interaction
ENSG00000157653	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000148229	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10118275	0.81[ASN][1000 genomes]
rs10124515	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10759640	0.80[ASN][1000 genomes]
rs10817476	0.81[CHB][hapmap]
rs10981713	0.81[CHB][hapmap]
rs10981714	0.81[CHB][hapmap]
rs10981719	0.81[CHB][hapmap]
rs10981734	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs10981762	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12350131	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16932730	0.85[CHB][hapmap];0.86[ASN][1000 genomes]
rs1998504	0.83[ASN][1000 genomes]
rs2093691	0.82[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2296073	0.82[CHB][hapmap]
rs2296075	0.85[CHB][hapmap];0.82[CHD][hapmap];0.85[ASN][1000 genomes]
rs35772163	0.84[ASN][1000 genomes]
rs6478006	0.86[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs7025770	0.80[ASN][1000 genomes]
rs7048039	0.83[ASN][1000 genomes]
rs7849513	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs7850002	0.81[ASN][1000 genomes]
rs7850003	0.88[ASN][1000 genomes]
rs7860625	0.91[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs7863921	0.80[ASN][1000 genomes]
rs7868271	0.82[CHB][hapmap];0.89[JPT][hapmap]

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	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv519849	chr9:116111407-116144973	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7873862	IKBKAP	cis	cerebellum	SCAN
rs7873862	BSPRY	cis	lymphoblastoid	seeQTL
rs7873862	BSPRY	cis	multi-tissue	Pritchard
rs7873862	ENSG00000119411	cis	multi-tissue	Pritchard
rs7873862	ORM1	cis	cerebellum	SCAN
rs7873862	HDHD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116111400-116113600	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr9:116111400-116114000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr9:116111800-116113600	Active TSS	Gastric	stomach
4	chr9:116112000-116113400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr9:116112000-116113400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
6	chr9:116112000-116114000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:116112200-116113600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr9:116112200-116113600	Enhancers	Spleen	Spleen
9	chr9:116112200-116113800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr9:116112200-116113800	Flanking Active TSS	GM12878-XiMat	blood
11	chr9:116112400-116113600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
12	chr9:116112400-116113600	Bivalent Enhancer	Fetal Thymus	thymus
13	chr9:116112400-116113800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr9:116112600-116113400	Bivalent Enhancer	Thymus	Thymus
15	chr9:116112600-116113600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:116112600-116113600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
17	chr9:116112600-116113800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
18	chr9:116112600-116113800	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr9:116112600-116113800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
20	chr9:116112600-116114000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr9:116112800-116113400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:116112800-116113400	Enhancers	Esophagus	oesophagus
23	chr9:116112800-116113800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
24	chr9:116112800-116113800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:116112800-116113800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
26	chr9:116112800-116114000	Bivalent Enhancer	HepG2	liver
27	chr9:116112800-116115400	Enhancers	Stomach Mucosa	stomach
28	chr9:116112800-116122800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:116113000-116113400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr9:116113000-116113400	Enhancers	H9 Cell Line	embryonic stem cell
31	chr9:116113000-116113400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr9:116113000-116113400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
33	chr9:116113000-116113400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:116113000-116113400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
35	chr9:116113000-116113400	Active TSS	Brain Anterior Caudate	brain
36	chr9:116113000-116113800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
37	chr9:116113000-116113800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr9:116113000-116114000	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr9:116113000-116114000	Enhancers	Primary B cells from peripheral blood	blood
40	chr9:116113000-116114000	Enhancers	Pancreas	Pancrea
41	chr9:116113000-116135600	Weak transcription	Colonic Mucosa	Colon
42	chr9:116113000-116138000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:116113200-116113400	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr9:116113200-116113400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
45	chr9:116113200-116113400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
46	chr9:116113200-116113400	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
47	chr9:116113200-116113400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
48	chr9:116113200-116113400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
49	chr9:116113200-116113400	Bivalent Enhancer	HUVEC	blood vessel
50	chr9:116113200-116113600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links