Variant report

Variant	rs7857616
Chromosome Location	chr9:94004897-94004898
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:94003518..94005912-chr9:94006715..94009331,2	MCF-7	breast:
2	chr9:93998370..94000905-chr9:94003934..94005756,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10991837	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10991844	0.85[CHB][hapmap]
rs10991848	0.86[EUR][1000 genomes]
rs10991849	0.86[EUR][1000 genomes]
rs10991853	1.00[CEU][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs10991854	0.85[CHB][hapmap]
rs10991885	0.85[CHB][hapmap]
rs10991886	0.85[CHB][hapmap]
rs10991887	0.85[CHB][hapmap]
rs10991894	0.85[CHB][hapmap]
rs10991897	0.85[CHB][hapmap]
rs10991900	1.00[CEU][hapmap];0.86[MEX][hapmap]
rs10991901	0.85[CHB][hapmap]
rs10991904	0.85[CHB][hapmap]
rs10991906	0.85[CHB][hapmap]
rs12683737	1.00[CEU][hapmap]
rs1397575	1.00[CEU][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16907311	0.85[CHB][hapmap]
rs16907358	0.83[EUR][1000 genomes]
rs1848984	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs1877125	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55642352	0.83[EUR][1000 genomes]
rs6479337	1.00[CEU][hapmap]
rs7020893	0.94[CEU][hapmap];0.86[MEX][hapmap]
rs7028794	0.85[EUR][1000 genomes]
rs7031965	0.81[EUR][1000 genomes]
rs7849152	0.85[EUR][1000 genomes]
rs7852888	0.83[EUR][1000 genomes]
rs7866204	0.87[EUR][1000 genomes]
rs7868501	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9792678	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893570	chr9:93973938-94148084	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482877	chr9:93979351-94157734	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7857616	ECM2	cis	parietal	SCAN
rs7857616	BARX1	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93970400-94005400	Weak transcription	Aorta	Aorta
2	chr9:93971000-94007800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:93971400-94009400	Weak transcription	Spleen	Spleen
4	chr9:93971800-94008000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr9:93972800-94009200	Weak transcription	Brain Germinal Matrix	brain
6	chr9:93975800-94005000	Weak transcription	Fetal Kidney	kidney
7	chr9:93980600-94007600	Weak transcription	Primary B cells from cord blood	blood
8	chr9:93981600-94008000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:93981600-94008000	Weak transcription	Esophagus	oesophagus
10	chr9:93982600-94008200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:93982800-94032400	Weak transcription	Ovary	ovary
12	chr9:93983000-94005600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:93983000-94008200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr9:93983000-94009000	Weak transcription	Fetal Lung	lung
15	chr9:93983000-94027000	Weak transcription	Fetal Intestine Large	intestine
16	chr9:93983000-94054000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr9:93983200-94005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:93983200-94015400	Weak transcription	Thymus	Thymus
19	chr9:93983200-94015800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr9:93983200-94027800	Weak transcription	Adipose Nuclei	Adipose
21	chr9:93983800-94010800	Weak transcription	Stomach Smooth Muscle	stomach
22	chr9:93984000-94052200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:93984000-94054600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr9:93984200-94024000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:93984400-94026200	Weak transcription	Primary T cells from cord blood	blood
26	chr9:93993400-94008400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr9:93995600-94009200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr9:93995800-94018600	Weak transcription	Fetal Intestine Small	intestine
29	chr9:93995800-94052400	Weak transcription	Fetal Stomach	stomach
30	chr9:93996800-94012400	Weak transcription	HSMMtube	muscle
31	chr9:93999200-94015800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:94000800-94011200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:94001000-94007600	Weak transcription	NHLF	lung
34	chr9:94001200-94007400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr9:94001400-94008000	Weak transcription	Brain Substantia Nigra	brain
36	chr9:94001800-94005400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:94001800-94008000	Weak transcription	Brain Angular Gyrus	brain
38	chr9:94002000-94007400	Weak transcription	Lung	lung
39	chr9:94002200-94007600	Weak transcription	Stomach Mucosa	stomach
40	chr9:94002600-94005600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr9:94002800-94032600	Weak transcription	Placenta	Placenta
42	chr9:94003200-94007600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:94003400-94007400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr9:94003600-94007800	Weak transcription	Right Ventricle	heart
45	chr9:94004000-94008000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:94004200-94005000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr9:94004200-94006000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:94004200-94007600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr9:94004200-94008000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:94004600-94005600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links