Variant report

Variant	rs4725068
Chromosome Location	chr7:8127710-8127711
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	chr7:8008014..8012241-chr7:8127326..8131877,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10226050	0.89[YRI][hapmap]
rs10229643	0.86[YRI][hapmap]
rs10241457	0.93[TSI][hapmap];0.93[YRI][hapmap]
rs10243846	0.93[YRI][hapmap]
rs10246564	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10273241	0.93[YRI][hapmap]
rs10486205	0.86[YRI][hapmap]
rs11976862	0.81[CEU][hapmap];0.89[YRI][hapmap]
rs12702693	0.82[CEU][hapmap];0.83[YRI][hapmap]
rs17568389	0.86[YRI][hapmap]
rs2058277	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2109382	0.81[CEU][hapmap]
rs2191321	0.96[YRI][hapmap]
rs3735457	0.92[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37977	0.88[TSI][hapmap];0.89[YRI][hapmap]
rs37981	0.91[TSI][hapmap];0.93[YRI][hapmap]
rs37988	0.86[YRI][hapmap]
rs37994	0.84[TSI][hapmap]
rs37995	0.86[TSI][hapmap];0.89[YRI][hapmap]
rs37998	0.92[LWK][hapmap];0.86[TSI][hapmap];0.93[YRI][hapmap]
rs37999	0.92[YRI][hapmap]
rs38001	0.81[AMR][1000 genomes]
rs38002	0.96[YRI][hapmap]
rs38003	0.96[YRI][hapmap]
rs38004	0.81[AMR][1000 genomes]
rs38012	0.86[TSI][hapmap];0.82[YRI][hapmap]
rs38013	0.89[TSI][hapmap];0.82[YRI][hapmap]
rs38014	0.86[YRI][hapmap]
rs38018	0.91[TSI][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs38019	0.89[YRI][hapmap];0.81[AMR][1000 genomes]
rs38021	0.81[AMR][1000 genomes]
rs38022	0.82[YRI][hapmap]
rs4140809	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4236406	0.86[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4720761	0.93[TSI][hapmap];0.93[YRI][hapmap]
rs4725060	0.86[YRI][hapmap]
rs9692283	0.96[YRI][hapmap]

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
rs4725068	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8067000-8135400	Weak transcription	Pancreas	Pancrea
2	chr7:8075600-8131800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:8085200-8128400	Weak transcription	Small Intestine	intestine
4	chr7:8091400-8127800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:8094000-8127800	Weak transcription	HSMM	muscle
6	chr7:8095400-8129600	Weak transcription	Gastric	stomach
7	chr7:8096000-8151600	Weak transcription	Spleen	Spleen
8	chr7:8102800-8130000	Weak transcription	Fetal Lung	lung
9	chr7:8103000-8127800	Weak transcription	Fetal Brain Female	brain
10	chr7:8103000-8128000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr7:8103000-8135400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr7:8103200-8131400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr7:8106600-8128200	Weak transcription	Osteobl	bone
14	chr7:8109000-8128400	Weak transcription	Brain Substantia Nigra	brain
15	chr7:8109000-8131800	Weak transcription	Fetal Muscle Leg	muscle
16	chr7:8109000-8132800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr7:8109200-8128400	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:8109200-8130400	Weak transcription	Brain Anterior Caudate	brain
19	chr7:8109200-8133400	Weak transcription	Fetal Intestine Small	intestine
20	chr7:8109200-8145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:8109400-8128000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:8109400-8128400	Weak transcription	Right Ventricle	heart
23	chr7:8112400-8128000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr7:8115400-8130400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr7:8123200-8130800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr7:8123400-8128400	Strong transcription	Dnd41	blood
27	chr7:8123400-8132000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr7:8123600-8127800	Strong transcription	Primary B cells from peripheral blood	blood
29	chr7:8123600-8128800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr7:8123600-8131800	Weak transcription	HMEC	breast
31	chr7:8123800-8129400	Strong transcription	GM12878-XiMat	blood
32	chr7:8123800-8132200	Strong transcription	Primary B cells from cord blood	blood
33	chr7:8124000-8127800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr7:8124200-8127800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr7:8124200-8129200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:8124200-8130400	Strong transcription	Fetal Thymus	thymus
37	chr7:8124400-8129000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:8124400-8129400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr7:8124800-8129000	Weak transcription	Fetal Kidney	kidney
40	chr7:8124800-8130200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr7:8125000-8130000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:8125000-8136400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr7:8125200-8132000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr7:8125400-8131400	Weak transcription	NH-A	brain
45	chr7:8125400-8132000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr7:8125400-8136800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr7:8126000-8128400	Weak transcription	NHDF-Ad	bronchial
48	chr7:8126000-8133400	Weak transcription	Hela-S3	cervix
49	chr7:8126200-8127800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:8126200-8127800	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links