Variant report

Variant	rs12201987
Chromosome Location	chr6:143182396-143182397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143175982..143177765-chr6:143180458..143183206,2	MCF-7	breast:
2	chr6:143181174..143183463-chr6:143265062..143267510,2	MCF-7	breast:
3	chr6:143181658..143183729-chr6:143211495..143213124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11155265	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11969311	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12190015	0.82[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs12190804	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12192692	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12194338	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12194808	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12196693	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12199711	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12205948	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12206012	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208876	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12210048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12210301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12214573	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444447	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs198661	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2142938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2184364	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876528	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4349826	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4492208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430707	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62430709	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62430712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430713	0.95[EUR][1000 genomes]
rs62432360	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62432362	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6905453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6912129	0.86[CEU][hapmap];0.84[AMR][1000 genomes]
rs6925118	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927858	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs728589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72990282	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72995085	0.88[EUR][1000 genomes]
rs7758383	0.86[ASN][1000 genomes]
rs972119	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998313	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv538459	chr6:143165802-143360098	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143168400-143188600	Weak transcription	Aorta	Aorta
2	chr6:143173200-143182400	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:143173200-143188600	Weak transcription	Fetal Intestine Small	intestine
4	chr6:143173600-143188200	Weak transcription	NHLF	lung
5	chr6:143175400-143182800	Weak transcription	Right Ventricle	heart
6	chr6:143175400-143185200	Weak transcription	Right Atrium	heart
7	chr6:143175600-143192000	Weak transcription	NHEK	skin
8	chr6:143175600-143192200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr6:143175600-143192800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:143176200-143182800	Weak transcription	Small Intestine	intestine
11	chr6:143176200-143185000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:143176600-143185200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr6:143176600-143186800	Weak transcription	Esophagus	oesophagus
14	chr6:143176600-143188200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr6:143176600-143192400	Weak transcription	NHDF-Ad	bronchial
16	chr6:143177000-143192200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:143177800-143182400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:143177800-143185000	Weak transcription	Fetal Kidney	kidney
19	chr6:143178000-143184800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:143178200-143192800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:143178800-143184800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr6:143179000-143184800	Weak transcription	Brain Substantia Nigra	brain
23	chr6:143179200-143182800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:143179200-143183400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:143179400-143183000	Weak transcription	Brain Angular Gyrus	brain
26	chr6:143179400-143184800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr6:143179400-143184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr6:143179400-143184800	Weak transcription	Psoas Muscle	Psoas
29	chr6:143179400-143186000	Weak transcription	Brain Germinal Matrix	brain
30	chr6:143179400-143188400	Weak transcription	Brain Hippocampus Middle	brain
31	chr6:143179600-143182400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:143179600-143182800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr6:143179600-143183000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr6:143179600-143183000	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:143179600-143183400	Enhancers	Primary T cells from cord blood	blood
36	chr6:143179600-143183400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:143179600-143183400	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:143179600-143183400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:143179600-143183400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr6:143179600-143185200	Weak transcription	Brain Anterior Caudate	brain
41	chr6:143179600-143185200	Weak transcription	Brain Cingulate Gyrus	brain
42	chr6:143179600-143185200	Weak transcription	Left Ventricle	heart
43	chr6:143179600-143185200	Weak transcription	Pancreas	Pancrea
44	chr6:143179600-143187000	Weak transcription	Fetal Stomach	stomach
45	chr6:143179600-143187800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr6:143179600-143188000	Weak transcription	HSMMtube	muscle
47	chr6:143179600-143188600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:143179600-143188600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:143179600-143189200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr6:143179600-143191200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links