Variant report

Variant	rs188953
Chromosome Location	chr3:51982251-51982252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:51980605..51983550-chr3:51988202..51990542,2	MCF-7	breast:
2	chr3:51975203..51979245-chr3:51981875..51985291,4	K562	blood:
3	chr3:51976380..51978109-chr3:51981388..51983019,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114767	Chromatin interaction
ENSG00000041880	Chromatin interaction
ENSG00000180929	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11926611	1.00[CEU][hapmap]
rs1566941	0.85[EUR][1000 genomes]
rs2015691	0.81[MKK][hapmap]
rs2271069	0.85[EUR][1000 genomes]
rs323864	0.81[AFR][1000 genomes]
rs323865	0.81[ASW][hapmap]
rs323867	0.81[ASW][hapmap]
rs323868	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes]
rs323871	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs323873	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs323874	0.81[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs323879	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs323885	0.87[AFR][1000 genomes]
rs323886	1.00[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs323887	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[LWK][hapmap];0.88[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs323892	0.81[MKK][hapmap]
rs323893	0.81[ASW][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs323895	0.81[ASW][hapmap];0.85[MKK][hapmap];0.92[YRI][hapmap]
rs323897	0.81[MKK][hapmap]
rs323898	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs3755797	0.85[EUR][1000 genomes]
rs3774344	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs411209	1.00[CEU][hapmap]
rs4986825	1.00[CEU][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520211	chr3:51772347-52166147	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012847	chr3:51811062-52056727	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
3	nsv536571	chr3:51811062-52056727	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
4	nsv1003453	chr3:51962081-52099441	Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv1804090	chr3:51962081-52140591	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv1835339	chr3:51962081-52140591	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv1003581	chr3:51973395-52108645	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	nsv1001062	chr3:51973395-52134638	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
9	nsv876780	chr3:51981021-52101799	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51977200-51983000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:51977200-51987600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:51977200-51989200	Weak transcription	Ovary	ovary
4	chr3:51977200-51992000	Weak transcription	Aorta	Aorta
5	chr3:51977400-51986200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:51977400-51987200	Weak transcription	Fetal Lung	lung
7	chr3:51977400-51989200	Weak transcription	Esophagus	oesophagus
8	chr3:51977600-51982400	Weak transcription	A549	lung
9	chr3:51977600-51982800	Weak transcription	GM12878-XiMat	blood
10	chr3:51977600-51983400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:51977600-51984400	Weak transcription	HepG2	liver
12	chr3:51977600-51986000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:51977600-51987200	Weak transcription	HSMMtube	muscle
14	chr3:51977600-51987600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:51977600-51987600	Weak transcription	HSMM	muscle
16	chr3:51977600-51989000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:51977600-51989000	Weak transcription	Pancreas	Pancrea
18	chr3:51977600-51989400	Weak transcription	Left Ventricle	heart
19	chr3:51977800-51983600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:51977800-51984000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:51977800-51985600	Weak transcription	Stomach Mucosa	stomach
22	chr3:51977800-51986000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:51977800-51987200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:51977800-51987800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:51977800-51989400	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:51978200-51982400	Strong transcription	Fetal Intestine Small	intestine
27	chr3:51978200-51983400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr3:51978200-51983600	Strong transcription	Fetal Stomach	stomach
29	chr3:51978200-51983600	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:51978200-51983600	Strong transcription	Spleen	Spleen
31	chr3:51978200-51983800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:51978200-51984200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:51978400-51982400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr3:51978400-51983400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:51978400-51984400	Strong transcription	Liver	Liver
36	chr3:51978600-51982800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:51978600-51983400	Strong transcription	Brain Anterior Caudate	brain
38	chr3:51978600-51983600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:51978800-51982400	Weak transcription	Placenta	Placenta
40	chr3:51978800-51983600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:51978800-51985200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr3:51978800-51987000	Weak transcription	Hela-S3	cervix
43	chr3:51979000-51982400	Weak transcription	Primary T cells from cord blood	blood
44	chr3:51979000-51987200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:51979200-51986000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:51979600-51982400	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:51979800-51987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:51980400-51983000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:51980400-51983200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:51980400-51989400	Weak transcription	Right Ventricle	heart

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