Variant report

Variant	rs496587
Chromosome Location	chr11:107269006-107269007
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107265232..107267832-chr11:107267875..107270757,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10502091	0.84[YRI][hapmap]
rs1263296	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2432869	0.80[CEU][hapmap]
rs4564297	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473520	0.86[CEU][hapmap]
rs479411	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs502338	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525996	0.81[CEU][hapmap]
rs537322	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs550203	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs574134	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs574879	0.94[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs580224	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58122182	0.87[AFR][1000 genomes]
rs604170	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs606632	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs609775	0.81[YRI][hapmap]
rs622862	0.94[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs626280	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636080	0.83[ASW][hapmap];0.90[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs655380	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656675	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7121399	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs73547700	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1038368	chr11:107116577-107664181	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv541163	chr11:107116577-107664181	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv898373	chr11:107124903-107433835	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv832261	chr11:107145901-107321562	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	esv2756363	chr11:107189790-107376790	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
13	nsv556376	chr11:107250851-107486598	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv972069	chr11:107267292-107275251	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs496587	GUCY1A2	cis	cerebellum	SCAN
rs496587	CARD17	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107195000-107299200	Weak transcription	Colon Smooth Muscle	Colon
2	chr11:107241600-107327800	Weak transcription	HSMMtube	muscle
3	chr11:107252600-107281200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr11:107252600-107323800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:107255000-107327600	Weak transcription	Fetal Heart	heart
6	chr11:107256600-107298000	Weak transcription	Brain Substantia Nigra	brain
7	chr11:107256600-107327600	Weak transcription	NHDF-Ad	bronchial
8	chr11:107256800-107274800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr11:107257200-107269600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr11:107257200-107275000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:107258600-107281600	Weak transcription	Fetal Brain Male	brain
12	chr11:107258800-107277000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:107258800-107291800	Weak transcription	Colonic Mucosa	Colon
14	chr11:107258800-107324200	Weak transcription	Small Intestine	intestine
15	chr11:107259000-107280400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:107259200-107299600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:107259600-107323400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:107261600-107310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr11:107262000-107274200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:107262200-107272200	Weak transcription	Fetal Brain Female	brain
21	chr11:107262200-107274200	Weak transcription	Aorta	Aorta
22	chr11:107262200-107274400	Weak transcription	Esophagus	oesophagus
23	chr11:107262200-107324000	Weak transcription	Pancreas	Pancrea
24	chr11:107262400-107274200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:107262600-107269600	Weak transcription	Brain Germinal Matrix	brain
26	chr11:107262600-107285400	Weak transcription	Fetal Thymus	thymus
27	chr11:107262800-107269400	Weak transcription	GM12878-XiMat	blood
28	chr11:107262800-107275600	Weak transcription	Stomach Mucosa	stomach
29	chr11:107262800-107283600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:107262800-107284000	Weak transcription	Fetal Kidney	kidney
31	chr11:107263000-107269200	Weak transcription	Brain Hippocampus Middle	brain
32	chr11:107263200-107269200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr11:107263200-107269600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:107263200-107274200	Weak transcription	Thymus	Thymus
35	chr11:107263200-107274400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr11:107263200-107286000	Weak transcription	Placenta	Placenta
37	chr11:107263200-107309400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr11:107263200-107310200	Weak transcription	Psoas Muscle	Psoas
39	chr11:107263200-107310400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr11:107263400-107269400	Weak transcription	Fetal Lung	lung
41	chr11:107263400-107269600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:107263400-107274200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr11:107263400-107274200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:107263400-107279400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr11:107263400-107287000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:107263400-107287000	Weak transcription	HSMM	muscle
47	chr11:107263400-107298800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr11:107263600-107269200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr11:107263600-107269400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr11:107263600-107269400	Weak transcription	Duodenum Mucosa	Duodenum

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