Variant report

Variant	rs3213964
Chromosome Location	chr2:187540732-187540733
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187538048..187541049-chr7:7133355..7136702,3	MCF-7	breast:
2	chr2:187533999..187537755-chr2:187540182..187542423,3	K562	blood:
3	chr2:187534492..187537090-chr2:187539566..187542233,2	MCF-7	breast:
4	chr2:187532982..187536054-chr2:187540521..187542155,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10165992	0.88[CHB][hapmap]
rs1072901	0.88[CHB][hapmap]
rs10755000	0.83[ASN][1000 genomes]
rs10931253	0.91[ASN][1000 genomes]
rs12475476	0.94[CHB][hapmap]
rs12618322	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs12620821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13020260	0.88[CHB][hapmap]
rs13028008	0.85[ASN][1000 genomes]
rs1448427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs17406229	0.91[ASN][1000 genomes]
rs17406346	0.88[CHB][hapmap]
rs2121975	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2121976	0.88[CHB][hapmap]
rs2595395	0.88[CHB][hapmap]
rs2682873	0.88[CHB][hapmap]
rs34840521	0.83[ASN][1000 genomes]
rs35348196	0.83[ASN][1000 genomes]
rs3768785	0.88[CHB][hapmap]
rs3816375	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs4667108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs55961288	0.86[ASN][1000 genomes]
rs6705757	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs718259	0.88[CHB][hapmap]
rs7585442	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7585471	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap]
rs930657	1.00[CHB][hapmap];0.96[CHD][hapmap];0.81[ASN][1000 genomes]
rs9789704	0.85[ASN][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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3213964	FSIP2	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187501000-187548400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:187503400-187545000	Weak transcription	Hela-S3	cervix
3	chr2:187507800-187546600	Weak transcription	Small Intestine	intestine
4	chr2:187511400-187546600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr2:187511600-187545000	Strong transcription	Osteobl	bone
6	chr2:187513800-187546800	Strong transcription	NH-A	brain
7	chr2:187514600-187546200	Strong transcription	Placenta	Placenta
8	chr2:187516400-187543600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:187516600-187545400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:187518800-187547200	Strong transcription	HUVEC	blood vessel
11	chr2:187520000-187545000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:187523000-187546800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:187525000-187543200	Weak transcription	Thymus	Thymus
14	chr2:187525400-187541800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:187527600-187543600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:187527600-187546400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:187527800-187542000	Strong transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:187527800-187542000	Strong transcription	HMEC	breast
19	chr2:187527800-187544200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:187528000-187543200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:187528000-187544000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr2:187528000-187544600	Strong transcription	HSMM	muscle
23	chr2:187528000-187548000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr2:187528200-187543600	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:187528400-187542600	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr2:187528600-187543600	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr2:187529000-187541600	Strong transcription	Fetal Thymus	thymus
28	chr2:187529000-187542400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr2:187529000-187548200	Weak transcription	Stomach Mucosa	stomach
30	chr2:187529200-187541800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr2:187529200-187541800	Strong transcription	Left Ventricle	heart
32	chr2:187529200-187542000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:187529200-187542200	Strong transcription	Ovary	ovary
34	chr2:187529200-187542600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr2:187531800-187541800	Strong transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:187531800-187543600	Strong transcription	Fetal Lung	lung
37	chr2:187532000-187540800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr2:187533200-187543600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:187533600-187541400	Strong transcription	Colon Smooth Muscle	Colon
40	chr2:187534400-187542200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:187536200-187543800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:187536200-187546800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:187536200-187548200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:187536400-187541600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr2:187536400-187543400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:187536400-187550000	Weak transcription	Gastric	stomach
47	chr2:187536600-187541800	Weak transcription	NHLF	lung
48	chr2:187537000-187543200	Weak transcription	Esophagus	oesophagus
49	chr2:187537000-187543600	Weak transcription	Pancreas	Pancrea
50	chr2:187537400-187541000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links