Variant report

Variant	rs2275998
Chromosome Location	chr11:66326581-66326582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:66324925..66326614-chr11:66329885..66331523,2	MCF-7	breast:
2	chr11:66325723..66328064-chr11:66383615..66385386,2	K562	blood:
3	chr11:66311873..66314750-chr11:66320969..66327300,6	K562	blood:
4	chr11:66325010..66327957-chr11:66384615..66387418,2	K562	blood:
5	chr11:66311617..66317579-chr11:66325496..66333927,8	MCF-7	breast:
6	chr11:66317473..66319701-chr11:66325756..66327731,2	K562	blood:

Variant related genes	Relation type
ENSG00000248643	Chromatin interaction
ENSG00000248746	Chromatin interaction
ENSG00000239306	Chromatin interaction
ENSG00000174165	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10896128	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11227532	0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11227539	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs11227554	0.80[CHD][hapmap];1.00[JPT][hapmap]
rs11227560	1.00[JPT][hapmap]
rs11227562	1.00[JPT][hapmap]
rs11227574	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs11550057	0.85[CEU][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs12223171	0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12223908	1.00[ASN][1000 genomes]
rs15969	0.85[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs2229455	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276136	1.00[JPT][hapmap]
rs3782080	0.90[ASN][1000 genomes]
rs3867132	1.00[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs3867133	0.85[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs57127845	0.89[EUR][1000 genomes]
rs59431265	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
4	nsv897787	chr11:66300348-66347850	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv897788	chr11:66319262-66347850	Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2275998	CTSF	cis	parietal	SCAN
rs2275998	CCND1	cis	parietal	SCAN
rs2275998	ESRRA	cis	cerebellum	SCAN
rs2275998	PACS1	cis	parietal	SCAN
rs2275998	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs2275998	SPTBN2	cis	cerebellum	SCAN
rs2275998	COX8A	cis	cerebellum	SCAN
rs2275998	CCS	cis	cerebellum	SCAN
rs2275998	UNC93B1	cis	cerebellum	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66314400-66327000	Weak transcription	Right Atrium	heart
2	chr11:66314800-66326600	Weak transcription	Psoas Muscle	Psoas
3	chr11:66319000-66337800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:66321400-66330400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:66321400-66331600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:66322600-66331400	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr11:66325000-66326600	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr11:66325000-66329200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr11:66325400-66327800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr11:66325800-66326800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:66326000-66328000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:66326200-66326600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr11:66326200-66326600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr11:66326200-66326600	Bivalent Enhancer	Brain Germinal Matrix	brain
15	chr11:66326200-66326600	Enhancers	Colon Smooth Muscle	Colon
16	chr11:66326200-66326800	Bivalent Enhancer	Duodenum Mucosa	Duodenum
17	chr11:66326200-66326800	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr11:66326200-66326800	Enhancers	Rectal Smooth Muscle	rectum
19	chr11:66326200-66327000	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
20	chr11:66326200-66327200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr11:66326200-66327400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr11:66326400-66326600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr11:66326400-66326600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr11:66326400-66326600	Bivalent Enhancer	Primary T cells from cord blood	blood
25	chr11:66326400-66326600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
26	chr11:66326400-66326600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
27	chr11:66326400-66326600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:66326400-66326600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:66326400-66326600	Enhancers	Brain Angular Gyrus	brain
30	chr11:66326400-66326600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr11:66326400-66326600	Enhancers	Brain Substantia Nigra	brain
32	chr11:66326400-66326600	Bivalent Enhancer	Fetal Heart	heart
33	chr11:66326400-66326600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr11:66326400-66326600	Enhancers	Ovary	ovary
35	chr11:66326400-66326600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
36	chr11:66326400-66326600	Bivalent Enhancer	Stomach Mucosa	stomach
37	chr11:66326400-66326600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
38	chr11:66326400-66326800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
39	chr11:66326400-66326800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr11:66326400-66326800	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr11:66326400-66326800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr11:66326400-66326800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
43	chr11:66326400-66326800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr11:66326400-66326800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:66326400-66326800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
46	chr11:66326400-66326800	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr11:66326400-66326800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr11:66326400-66326800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr11:66326400-66326800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr11:66326400-66326800	Enhancers	Adipose Nuclei	Adipose

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