Variant report

Variant	rs929509
Chromosome Location	chr7:8125964-8125965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10253260	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10257285	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265283	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10272512	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1468594	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2159510	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28177	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs35953256	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs37984	0.95[CEU][hapmap];0.83[AMR][1000 genomes]
rs37985	0.83[AMR][1000 genomes]
rs37990	0.95[CEU][hapmap];0.82[AMR][1000 genomes]
rs37991	0.87[AMR][1000 genomes]
rs38005	0.88[AMR][1000 genomes]
rs4725058	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4725063	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4725066	0.90[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4725067	0.90[YRI][hapmap]
rs4725069	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463754	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6463755	0.95[CEU][hapmap];0.86[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6974264	0.95[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975078	1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6975913	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6977376	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7777337	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795506	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798367	0.95[CEU][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7806440	0.96[AMR][1000 genomes];0.98[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	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
2	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
3	nsv1020686	chr7:8095118-8311985	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv538723	chr7:8095118-8311985	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1009766	chr7:8106112-8134286	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs929509	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8066400-8127600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr7:8066600-8126000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
4	chr7:8075000-8126800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr7:8085200-8128400	Weak transcription	Small Intestine	intestine
7	chr7:8091400-8127800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:8094000-8127800	Weak transcription	HSMM	muscle
9	chr7:8095400-8129600	Weak transcription	Gastric	stomach
10	chr7:8096000-8127600	Weak transcription	Esophagus	oesophagus
11	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
12	chr7:8102800-8130000	Weak transcription	Fetal Lung	lung
13	chr7:8103000-8127800	Weak transcription	Fetal Brain Female	brain
14	chr7:8103000-8128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr7:8103200-8131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr7:8106000-8126000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:8106200-8126200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr7:8106600-8128200	Weak transcription	Osteobl	bone
20	chr7:8107600-8126000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:8109000-8128400	Weak transcription	Brain Substantia Nigra	brain
22	chr7:8109000-8131800	Weak transcription	Fetal Muscle Leg	muscle
23	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:8109200-8128400	Weak transcription	Brain Hippocampus Middle	brain
25	chr7:8109200-8130400	Weak transcription	Brain Anterior Caudate	brain
26	chr7:8109200-8133400	Weak transcription	Fetal Intestine Small	intestine
27	chr7:8109200-8145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:8109400-8128000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr7:8109400-8128400	Weak transcription	Right Ventricle	heart
30	chr7:8110800-8126000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:8111200-8126000	Weak transcription	Ovary	ovary
32	chr7:8111200-8126000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:8111400-8126200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr7:8111800-8126200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:8112400-8128000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:8115400-8130400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr7:8116400-8126200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr7:8123200-8130800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr7:8123400-8128400	Strong transcription	Dnd41	blood
40	chr7:8123400-8132000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr7:8123600-8126200	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr7:8123600-8127800	Strong transcription	Primary B cells from peripheral blood	blood
43	chr7:8123600-8128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:8123600-8131800	Weak transcription	HMEC	breast
45	chr7:8123800-8129400	Strong transcription	GM12878-XiMat	blood
46	chr7:8123800-8132200	Strong transcription	Primary B cells from cord blood	blood
47	chr7:8124000-8127800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr7:8124200-8126400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:8124200-8127800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr7:8124200-8129200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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