Variant report

Variant	rs9655516
Chromosome Location	chr7:8071406-8071407
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8068288..8070626-chr7:8070654..8072447,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10226865	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10238003	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10253861	0.88[CEU][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10264999	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10278726	0.87[ASW][hapmap];1.00[CEU][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10278791	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10281919	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11981372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476823	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17568389	0.82[CEU][hapmap]
rs258850	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258852	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs37972	0.80[GIH][hapmap];0.83[TSI][hapmap]
rs37973	0.81[TSI][hapmap]
rs37974	0.88[MEX][hapmap]
rs37976	1.00[CEU][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37979	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs37982	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs37986	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37987	1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37997	0.85[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs38000	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs38007	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs38008	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs38009	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs38015	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4256496	1.00[CEU][hapmap]
rs4725055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4725056	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4725059	0.85[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6953808	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7796831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7808399	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7810540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv518779	chr7:8055664-8077359	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv1793794	chr7:8064509-8078802	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9655516	GLCCI1	cis	parietal	SCAN
rs9655516	LOC389458	cis	cerebellum	SCAN
rs9655516	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8036400-8077400	Weak transcription	Right Ventricle	heart
2	chr7:8036600-8074600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:8041600-8095000	Weak transcription	Gastric	stomach
4	chr7:8041800-8075400	Weak transcription	Brain Hippocampus Middle	brain
5	chr7:8043000-8099200	Weak transcription	Colon Smooth Muscle	Colon
6	chr7:8044600-8074400	Weak transcription	Brain Angular Gyrus	brain
7	chr7:8046800-8074400	Weak transcription	Brain Substantia Nigra	brain
8	chr7:8047400-8075600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:8047600-8108200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:8064400-8096200	Weak transcription	NHLF	lung
11	chr7:8065000-8074400	Weak transcription	Aorta	Aorta
12	chr7:8065000-8076800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:8065000-8095000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:8065000-8108600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr7:8066400-8074200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr7:8066400-8074400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr7:8066400-8074400	Weak transcription	Primary T cells from cord blood	blood
18	chr7:8066400-8074400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:8066400-8074400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr7:8066400-8074400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:8066400-8074600	Weak transcription	Lung	lung
22	chr7:8066400-8075200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:8066400-8075200	Weak transcription	Esophagus	oesophagus
24	chr7:8066400-8075600	Weak transcription	Fetal Kidney	kidney
25	chr7:8066400-8090800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:8066400-8096600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr7:8066600-8075200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr7:8066600-8075200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:8066600-8077000	Weak transcription	Fetal Heart	heart
31	chr7:8066600-8082000	Weak transcription	Osteobl	bone
32	chr7:8066600-8099800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr7:8066800-8074400	Weak transcription	Ovary	ovary
35	chr7:8066800-8074400	Weak transcription	Spleen	Spleen
36	chr7:8066800-8074600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:8066800-8074600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr7:8066800-8074600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:8066800-8074800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr7:8066800-8074800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr7:8066800-8074800	Weak transcription	Adipose Nuclei	Adipose
42	chr7:8066800-8075000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:8066800-8075400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr7:8066800-8075400	Weak transcription	Liver	Liver
45	chr7:8066800-8082600	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr7:8066800-8091200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr7:8066800-8095000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:8066800-8095600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr7:8066800-8099800	Weak transcription	Brain Anterior Caudate	brain
50	chr7:8066800-8108600	Weak transcription	Brain Cingulate Gyrus	brain

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