Variant report

Variant	rs12612708
Chromosome Location	chr2:20172554-20172555
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20171873..20173684-chr2:20189746..20192019,2	MCF-7	breast:
2	chr2:20171001..20173873-chr2:20178005..20179964,2	K562	blood:
3	chr2:20163553..20165863-chr2:20171853..20173573,2	K562	blood:

Variant related genes	Relation type
ENSG00000118965	Chromatin interaction
ENSG00000227210	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10165128	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10178256	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs10187524	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10190308	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10191437	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10197369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495700	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1115274	0.89[ASN][1000 genomes]
rs12477955	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12478934	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12616917	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1370587	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1437859	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1595414	0.95[CHB][hapmap];0.90[ASN][1000 genomes]
rs1595415	0.87[ASN][1000 genomes]
rs1824661	0.83[ASN][1000 genomes]
rs1947730	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2045779	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2242192	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28401180	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28598872	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731663	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs3820949	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4297843	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721864	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6736663	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741091	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7569975	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7572536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575732	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584726	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604699	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	esv1798392	chr2:20131079-20173255	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
2	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
3	chr2:20128400-20188400	Weak transcription	Colon Smooth Muscle	Colon
4	chr2:20128400-20189200	Weak transcription	Small Intestine	intestine
5	chr2:20129400-20184800	Weak transcription	Esophagus	oesophagus
6	chr2:20129600-20189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:20130200-20189000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:20130400-20188800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:20130600-20188800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:20131800-20189000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:20133600-20184800	Weak transcription	Psoas Muscle	Psoas
12	chr2:20133800-20173200	Weak transcription	NHEK	skin
13	chr2:20133800-20176800	Weak transcription	HMEC	breast
14	chr2:20136400-20177000	Weak transcription	GM12878-XiMat	blood
15	chr2:20136400-20177200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:20136600-20177200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:20136800-20188800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:20136800-20189000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:20138000-20177000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr2:20138200-20188800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr2:20138600-20184800	Weak transcription	Aorta	Aorta
22	chr2:20144600-20173200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:20144600-20173400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:20144600-20173600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:20145000-20176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:20145200-20188000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr2:20146000-20173200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr2:20148400-20174600	Weak transcription	NH-A	brain
29	chr2:20149600-20174800	Weak transcription	NHDF-Ad	bronchial
30	chr2:20152400-20173200	Weak transcription	Brain Anterior Caudate	brain
31	chr2:20152400-20173200	Weak transcription	HSMM	muscle
32	chr2:20153200-20177400	Weak transcription	Brain Germinal Matrix	brain
33	chr2:20153200-20184400	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:20156200-20174800	Weak transcription	Liver	Liver
35	chr2:20157800-20187200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:20159600-20173200	Weak transcription	Pancreas	Pancrea
37	chr2:20160600-20181200	Strong transcription	A549	lung
38	chr2:20161200-20173200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:20161600-20173200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:20161600-20176800	Weak transcription	HSMMtube	muscle
41	chr2:20161800-20173200	Weak transcription	Primary T cells from cord blood	blood
42	chr2:20162400-20188200	Weak transcription	Brain Substantia Nigra	brain
43	chr2:20163000-20173200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:20163200-20188800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:20164200-20187800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:20164600-20187000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:20164600-20189000	Weak transcription	Placenta	Placenta
48	chr2:20164800-20189000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr2:20165000-20181600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:20165000-20187000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links