Variant report

Variant	rs2231332
Chromosome Location	chr13:38924263-38924264
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:38923439..38924342-chr19:36630421..36631091,2	Hela-S3	cervix:
2	chr13:38921186..38924004-chr13:38924043..38925621,2	MCF-7	breast:
3	chr10:126604859..126605843-chr13:38923544..38924473,3	NB4	blood:
4	chr1:46806181..46806774-chr13:38923650..38924520,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000249456	Chromatin interaction
ENSG00000120686	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000117481	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10514844	1.00[CEU][hapmap]
rs11693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330963	1.00[CHB][hapmap]
rs1330964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330976	1.00[CEU][hapmap]
rs1360385	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576611	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231331	1.00[CEU][hapmap]
rs2455412	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481876	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485788	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2485789	1.00[CHB][hapmap];0.97[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496456	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496466	1.00[CHB][hapmap]
rs2496473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943581	0.83[ASN][1000 genomes]
rs4943583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943584	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943586	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326028	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326913	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332974	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335723	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338958	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532209	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532218	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603368	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986773	1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv561512	chr13:38881318-38930893	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv900005	chr13:38881318-38932949	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38922400-38925200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr13:38922600-38924800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr13:38922600-38925000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr13:38922600-38925000	Active TSS	K562	blood
5	chr13:38922600-38925200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr13:38922600-38925200	Active TSS	HSMMtube	muscle
7	chr13:38922600-38926000	Active TSS	Right Atrium	heart
8	chr13:38922800-38924400	Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr13:38922800-38924400	Active TSS	Thymus	Thymus
10	chr13:38922800-38924600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:38922800-38924600	Active TSS	Brain Cingulate Gyrus	brain
12	chr13:38922800-38924600	Active TSS	Brain Germinal Matrix	brain
13	chr13:38922800-38924600	Active TSS	Brain Substantia Nigra	brain
14	chr13:38922800-38924600	Active TSS	Rectal Smooth Muscle	rectum
15	chr13:38922800-38924600	Active TSS	Stomach Smooth Muscle	stomach
16	chr13:38922800-38924800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr13:38922800-38924800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:38922800-38924800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:38922800-38924800	Active TSS	Muscle Satellite Cultured Cells	--
20	chr13:38922800-38924800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr13:38922800-38924800	Active TSS	Fetal Kidney	kidney
22	chr13:38922800-38924800	Active TSS	Fetal Stomach	stomach
23	chr13:38922800-38925000	Active TSS	H1 Cell Line	embryonic stem cell
24	chr13:38922800-38925000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:38922800-38925000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr13:38922800-38925000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:38922800-38925000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr13:38922800-38925000	Active TSS	Aorta	Aorta
29	chr13:38922800-38925000	Active TSS	Fetal Intestine Large	intestine
30	chr13:38922800-38925000	Active TSS	GM12878-XiMat	blood
31	chr13:38922800-38925200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr13:38922800-38925200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:38922800-38925200	Active TSS	NHLF	lung
34	chr13:38922800-38926200	Active TSS	Right Ventricle	heart
35	chr13:38923000-38924400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr13:38923000-38924400	Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr13:38923000-38924600	Active TSS	Brain Anterior Caudate	brain
38	chr13:38923000-38924600	Active TSS	Colon Smooth Muscle	Colon
39	chr13:38923000-38924600	Active TSS	Fetal Heart	heart
40	chr13:38923000-38924800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr13:38923000-38924800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:38923000-38924800	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr13:38923000-38924800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr13:38923000-38924800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:38923000-38924800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr13:38923000-38924800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr13:38923000-38924800	Active TSS	Esophagus	oesophagus
48	chr13:38923000-38924800	Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr13:38923000-38924800	Active TSS	Small Intestine	intestine
50	chr13:38923000-38924800	Active TSS	Stomach Mucosa	stomach

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