Variant report

Variant	rs2496476
Chromosome Location	chr13:38921634-38921635
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	chr13:38915558..38922004-chr13:38925835..38933064,8	K562	blood:
2	chr13:38921186..38924004-chr13:38924043..38925621,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120686	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];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	1.00[CEU][hapmap];1.00[CHB][hapmap];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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576611	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[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];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231331	1.00[CEU][hapmap]
rs2231332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455412	0.81[AMR][1000 genomes];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];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485788	0.81[EUR][1000 genomes]
rs2485789	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496456	0.81[AMR][1000 genomes];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[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];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];0.89[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	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	0.87[AMR][1000 genomes];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	0.89[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];0.87[AMR][1000 genomes];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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	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:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38915800-38922400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr13:38915800-38922800	Weak transcription	Stomach Mucosa	stomach
3	chr13:38919600-38922800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:38920000-38922600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr13:38920200-38922600	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr13:38920200-38922600	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr13:38920200-38922800	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:38920200-38922800	Enhancers	NHEK	skin
9	chr13:38920200-38923000	Weak transcription	Psoas Muscle	Psoas
10	chr13:38920400-38922600	Weak transcription	Small Intestine	intestine
11	chr13:38920400-38922800	Weak transcription	NH-A	brain
12	chr13:38920400-38923000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:38920400-38923200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:38920600-38921800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr13:38920600-38922600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:38921200-38921800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:38921200-38922400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:38921400-38922600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr13:38921400-38922600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr13:38921400-38922600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:38921400-38922600	Enhancers	HMEC	breast
22	chr13:38921600-38922600	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr13:38921600-38922600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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