Variant report

Variant	rs7795506
Chromosome Location	chr7:8128944-8128945
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:8008014..8012241-chr7:8127326..8131877,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233108	Chromatin interaction
ENSG00000106415	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10253260	0.83[ASW][hapmap];0.88[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10257285	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10265283	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10272512	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1468594	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2159510	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28177	0.84[CEU][hapmap]
rs35953256	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs37984	0.88[CEU][hapmap];0.95[MEX][hapmap]
rs37990	0.88[CEU][hapmap]
rs37991	0.81[AMR][1000 genomes]
rs38005	0.83[AMR][1000 genomes]
rs4725058	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4725063	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4725066	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4725069	0.88[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463754	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6463755	0.88[CEU][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6974264	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6975078	0.92[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6975913	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6977376	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7777337	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7798367	0.88[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7806440	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs929509	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]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7795506	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL
rs7795506	GLCCI1	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
2	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:8095400-8129600	Weak transcription	Gastric	stomach
4	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
5	chr7:8102800-8130000	Weak transcription	Fetal Lung	lung
6	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
7	chr7:8103200-8131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:8109000-8131800	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:8109200-8130400	Weak transcription	Brain Anterior Caudate	brain
11	chr7:8109200-8133400	Weak transcription	Fetal Intestine Small	intestine
12	chr7:8109200-8145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:8115400-8130400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:8123200-8130800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr7:8123400-8132000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr7:8123600-8131800	Weak transcription	HMEC	breast
17	chr7:8123800-8129400	Strong transcription	GM12878-XiMat	blood
18	chr7:8123800-8132200	Strong transcription	Primary B cells from cord blood	blood
19	chr7:8124200-8129200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr7:8124200-8130400	Strong transcription	Fetal Thymus	thymus
21	chr7:8124400-8129000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:8124400-8129400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:8124800-8129000	Weak transcription	Fetal Kidney	kidney
24	chr7:8124800-8130200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:8125000-8130000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr7:8125000-8136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:8125200-8132000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr7:8125400-8131400	Weak transcription	NH-A	brain
29	chr7:8125400-8132000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:8125400-8136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:8126000-8133400	Weak transcription	Hela-S3	cervix
32	chr7:8126200-8133000	Weak transcription	Liver	Liver
33	chr7:8126200-8135200	Weak transcription	Fetal Stomach	stomach
34	chr7:8126200-8137200	Weak transcription	Left Ventricle	heart
35	chr7:8126400-8130200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:8126400-8131800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:8126400-8133800	Weak transcription	Fetal Intestine Large	intestine
38	chr7:8126400-8133800	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:8126400-8134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:8126400-8135000	Weak transcription	Thymus	Thymus
41	chr7:8126400-8135400	Weak transcription	Fetal Heart	heart
42	chr7:8126600-8131200	Weak transcription	Placenta	Placenta
43	chr7:8126600-8132200	Weak transcription	Adipose Nuclei	Adipose
44	chr7:8127000-8130200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:8127000-8130600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:8127000-8132600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:8127000-8138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:8127000-8138200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:8127200-8131800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr7:8127200-8132000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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