Variant report

Variant	rs4725069
Chromosome Location	chr7:8132252-8132253
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:8008233..8010906-chr7:8131128..8133418,2	MCF-7	breast:
2	chr7:8121598..8125026-chr7:8129163..8132409,4	MCF-7	breast:
3	chr7:8123610..8126481-chr7:8130672..8132477,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10253260	0.91[ASW][hapmap];0.92[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs10257285	0.92[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10265283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272512	0.92[CEU][hapmap]
rs1468594	0.83[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs2159510	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28177	0.88[CEU][hapmap]
rs35953256	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs37984	0.92[CEU][hapmap];0.90[MEX][hapmap]
rs37990	0.92[CEU][hapmap]
rs4725058	0.80[EUR][1000 genomes]
rs4725066	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6463754	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6463755	0.83[ASW][hapmap];0.92[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6974264	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6975078	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6975913	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6977376	0.85[EUR][1000 genomes]
rs7777337	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7795506	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]
rs7798367	0.92[CEU][hapmap];0.86[MEX][hapmap]
rs7806440	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs929509	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]

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
rs4725069	GLCCI1	cis	parietal	SCAN
rs4725069	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
2	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
3	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:8109200-8133400	Weak transcription	Fetal Intestine Small	intestine
6	chr7:8109200-8145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:8125000-8136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:8125400-8136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr7:8126000-8133400	Weak transcription	Hela-S3	cervix
10	chr7:8126200-8133000	Weak transcription	Liver	Liver
11	chr7:8126200-8135200	Weak transcription	Fetal Stomach	stomach
12	chr7:8126200-8137200	Weak transcription	Left Ventricle	heart
13	chr7:8126400-8133800	Weak transcription	Fetal Intestine Large	intestine
14	chr7:8126400-8133800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr7:8126400-8134800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:8126400-8135000	Weak transcription	Thymus	Thymus
17	chr7:8126400-8135400	Weak transcription	Fetal Heart	heart
18	chr7:8127000-8132600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr7:8127000-8138000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:8127000-8138200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:8127200-8132400	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr7:8127200-8134200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr7:8127200-8136200	Weak transcription	Brain Germinal Matrix	brain
24	chr7:8127600-8134200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr7:8127800-8135800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:8127800-8137400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr7:8127800-8138000	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr7:8127800-8144600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:8128400-8136800	Weak transcription	Dnd41	blood
30	chr7:8129200-8144000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:8129400-8133600	Weak transcription	GM12878-XiMat	blood
32	chr7:8129400-8135000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:8129600-8132800	Strong transcription	Primary T cells from cord blood	blood
34	chr7:8130200-8133000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr7:8130400-8133800	Weak transcription	HepG2	liver
36	chr7:8130400-8135000	Weak transcription	Fetal Thymus	thymus
37	chr7:8131600-8132800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr7:8131800-8132400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr7:8131800-8132800	Enhancers	HMEC	breast
40	chr7:8131800-8133000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:8132000-8132400	Enhancers	Psoas Muscle	Psoas
42	chr7:8132000-8132400	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:8132000-8132600	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr7:8132000-8132800	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr7:8132000-8132800	Enhancers	NHEK	skin
46	chr7:8132200-8132400	Enhancers	Adipose Nuclei	Adipose
47	chr7:8132200-8132600	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr7:8132200-8134400	Weak transcription	HSMMtube	muscle
49	chr7:8132200-8137800	Weak transcription	Primary B cells from cord blood	blood

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