Variant report

Variant	rs10193212
Chromosome Location	chr2:191334424-191334425
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	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:
2	chr2:191272262..191274939-chr2:191333629..191335814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction
ENSG00000272979	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10182754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931452	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12473460	0.83[YRI][hapmap]
rs12475614	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12613365	0.83[YRI][hapmap]
rs12613807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12622496	0.87[YRI][hapmap]
rs12693574	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693575	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693576	0.83[YRI][hapmap]
rs12998288	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs13019278	0.83[YRI][hapmap]
rs13020324	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13409841	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2354878	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35095338	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3811607	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811609	0.83[YRI][hapmap]
rs4264585	0.83[YRI][hapmap]
rs4324342	0.83[YRI][hapmap]
rs4340549	0.85[LWK][hapmap]
rs4853507	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4853702	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4853705	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4853711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4853713	0.84[CHB][hapmap];0.95[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434391	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707691	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6707773	0.83[YRI][hapmap]
rs6711006	0.83[YRI][hapmap]
rs7557681	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7564829	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596573	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9646748	0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9646815	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10193212	FLJ20160	cis	multi-tissue	Pritchard
rs10193212	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs10193212	MFSD6	cis	Artery Tibial	GTEx
rs10193212	TMEM194B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
2	chr2:191322000-191335800	Weak transcription	Esophagus	oesophagus
3	chr2:191322600-191335600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:191323000-191334600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:191323200-191335800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:191325600-191335800	Weak transcription	Lung	lung
7	chr2:191325600-191346200	Weak transcription	Right Ventricle	heart
8	chr2:191327600-191353000	Weak transcription	Primary B cells from cord blood	blood
9	chr2:191328800-191334600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr2:191329600-191334600	Weak transcription	Thymus	Thymus
11	chr2:191330000-191334800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:191330200-191334800	Enhancers	K562	blood
13	chr2:191330600-191335200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:191330800-191334800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr2:191330800-191335400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:191330800-191335400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr2:191331000-191334800	Enhancers	NHDF-Ad	bronchial
18	chr2:191331000-191335000	Enhancers	Brain Substantia Nigra	brain
19	chr2:191331000-191335200	Enhancers	Brain Cingulate Gyrus	brain
20	chr2:191331000-191335400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:191331000-191335400	Enhancers	Hela-S3	cervix
22	chr2:191331000-191335400	Enhancers	Osteobl	bone
23	chr2:191331200-191335400	Enhancers	NHLF	lung
24	chr2:191331200-191335600	Enhancers	Fetal Lung	lung
25	chr2:191331400-191334800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:191331400-191334800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr2:191331400-191335000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:191331400-191335000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:191331400-191335200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:191331400-191335200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:191331400-191335400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:191331400-191335400	Enhancers	Brain Angular Gyrus	brain
33	chr2:191331400-191335400	Enhancers	Fetal Heart	heart
34	chr2:191331400-191335400	Enhancers	Fetal Muscle Leg	muscle
35	chr2:191331400-191335400	Enhancers	Fetal Stomach	stomach
36	chr2:191331400-191335600	Enhancers	Colon Smooth Muscle	Colon
37	chr2:191331600-191334600	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:191331600-191334800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:191331600-191334800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:191331600-191334800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:191331600-191335000	Genic enhancers	Primary T cells from cord blood	blood
42	chr2:191331600-191335400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr2:191331600-191335400	Enhancers	Stomach Mucosa	stomach
44	chr2:191331600-191335600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:191331800-191335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:191332400-191334800	Enhancers	Duodenum Mucosa	Duodenum
47	chr2:191332400-191334800	Enhancers	NH-A	brain
48	chr2:191332400-191335400	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr2:191332400-191335400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:191332400-191335400	Enhancers	Fetal Intestine Small	intestine

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