Variant report

Variant	rs3862796
Chromosome Location	chr11:72705522-72705523
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:72694533..72697472-chr11:72703924..72706266,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10793048	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs10898885	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10898889	0.81[AFR][1000 genomes]
rs11235620	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11822039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12294037	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs12419915	0.89[AFR][1000 genomes]
rs12805658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12808517	0.82[ASW][hapmap];0.91[CEU][hapmap]
rs1612659	0.90[ASN][1000 genomes]
rs1783575	0.93[GIH][hapmap]
rs2187494	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2366256	0.90[ASN][1000 genomes]
rs3862794	0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs4394861	0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs4400839	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.98[ASN][1000 genomes]
rs4944016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4944804	0.82[ASW][hapmap]
rs593753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592500	0.92[CEU][hapmap]
rs6592505	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592509	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.91[ASN][1000 genomes]
rs6592510	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs7102253	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7108955	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs7946861	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3862796	MYEOV	cis	parietal	SCAN
rs3862796	FGF4	cis	cerebellum	SCAN
rs3862796	ATG16L2	cis	parietal	SCAN
rs3862796	STARD10	cis	Whole Blood	GTEx
rs3862796	KCNE3	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72636400-72712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:72637000-72721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:72649000-72721600	Weak transcription	Thymus	Thymus
4	chr11:72666600-72721600	Weak transcription	Lung	lung
5	chr11:72669800-72721800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:72673000-72708000	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:72681800-72720200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr11:72682000-72710600	Weak transcription	Aorta	Aorta
9	chr11:72682800-72721600	Weak transcription	Right Ventricle	heart
10	chr11:72683000-72706600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:72684000-72712800	Weak transcription	Small Intestine	intestine
12	chr11:72684000-72721600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr11:72686600-72721600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:72687600-72708600	Weak transcription	NHDF-Ad	bronchial
15	chr11:72687600-72722200	Weak transcription	NHLF	lung
16	chr11:72687600-72724200	Weak transcription	HMEC	breast
17	chr11:72688400-72706200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:72688600-72721600	Weak transcription	Brain Germinal Matrix	brain
19	chr11:72689800-72706800	Weak transcription	Esophagus	oesophagus
20	chr11:72689800-72717800	Weak transcription	Psoas Muscle	Psoas
21	chr11:72689800-72718400	Weak transcription	Fetal Intestine Small	intestine
22	chr11:72693400-72721600	Weak transcription	Left Ventricle	heart
23	chr11:72693600-72708200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr11:72694400-72708000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:72695600-72720400	Weak transcription	Adipose Nuclei	Adipose
26	chr11:72695800-72720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:72696000-72715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr11:72696000-72720200	Weak transcription	Fetal Intestine Large	intestine
29	chr11:72696000-72720800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:72696000-72724000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:72696600-72708000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr11:72697000-72718400	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:72697000-72721600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr11:72697200-72710600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr11:72697200-72712600	Weak transcription	Fetal Lung	lung
36	chr11:72697200-72713400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:72697200-72720600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr11:72699200-72721600	Weak transcription	HSMM	muscle
39	chr11:72699400-72709400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr11:72699600-72713600	Weak transcription	Placenta	Placenta
41	chr11:72699600-72720200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr11:72700000-72720800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:72700400-72719800	Weak transcription	Primary T cells from cord blood	blood
44	chr11:72700600-72718800	Weak transcription	Fetal Brain Female	brain
45	chr11:72700600-72720600	Weak transcription	Fetal Brain Male	brain
46	chr11:72700800-72711800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr11:72700800-72720400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr11:72701000-72712600	Weak transcription	A549	lung
49	chr11:72701000-72720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:72701000-72721600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links