Variant report

Variant	rs835487
Chromosome Location	chr12:105060767-105060768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105054651..105057049-chr12:105058504..105061225,2	MCF-7	breast:
2	chr12:105060606..105063528-chr12:105064614..105066569,2	K562	blood:
3	chr12:105053331..105055991-chr12:105057924..105061731,3	K562	blood:
4	chr12:105050512..105052954-chr12:105058253..105060916,2	K562	blood:
5	chr12:105056072..105057586-chr12:105059324..105062166,2	K562	blood:

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs835486	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs835488	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs835490	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835491	0.96[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs835492	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs835493	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs856595	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105038000-105062000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:105038400-105061200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr12:105038400-105062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:105038600-105061000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr12:105038600-105061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:105038600-105062400	Weak transcription	HMEC	breast
7	chr12:105038600-105062800	Weak transcription	Esophagus	oesophagus
8	chr12:105038600-105063200	Weak transcription	Primary T cells from cord blood	blood
9	chr12:105039200-105062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:105044600-105061600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:105046200-105061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:105046400-105061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:105048000-105062400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:105049200-105062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:105051000-105061800	Weak transcription	HSMMtube	muscle
16	chr12:105051000-105065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:105051800-105062000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:105051800-105062200	Weak transcription	Spleen	Spleen
19	chr12:105051800-105065000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:105052400-105061200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr12:105052400-105061400	Weak transcription	Lung	lung
22	chr12:105053000-105062200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:105054600-105061200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:105054600-105061800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:105055200-105061400	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr12:105055400-105062600	Genic enhancers	Dnd41	blood
27	chr12:105055600-105061400	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:105056000-105061000	Weak transcription	Gastric	stomach
29	chr12:105056000-105062600	Weak transcription	Small Intestine	intestine
30	chr12:105056200-105061000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:105056200-105061200	Weak transcription	Right Ventricle	heart
32	chr12:105056200-105062400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:105057800-105061200	Weak transcription	Primary B cells from cord blood	blood
34	chr12:105057800-105063000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:105058000-105063200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:105058400-105061400	Weak transcription	Thymus	Thymus
37	chr12:105058400-105062800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:105058800-105061000	Weak transcription	Fetal Heart	heart
39	chr12:105059000-105061200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr12:105059000-105061600	Weak transcription	Fetal Brain Male	brain
41	chr12:105059200-105063200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr12:105059400-105061000	Weak transcription	Fetal Stomach	stomach
43	chr12:105059400-105062200	Weak transcription	GM12878-XiMat	blood
44	chr12:105059600-105063000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:105060200-105061400	Enhancers	Stomach Smooth Muscle	stomach
46	chr12:105060200-105062000	Enhancers	Colon Smooth Muscle	Colon
47	chr12:105060200-105062400	Weak transcription	NH-A	brain
48	chr12:105060200-105068400	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr12:105060400-105061400	Weak transcription	Brain Germinal Matrix	brain
50	chr12:105060400-105061800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links