Variant report

Variant	rs4952913
Chromosome Location	chr2:48678659-48678660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48670330..48672555-chr2:48677413..48681489,3	MCF-7	breast:
2	chr2:48676760..48679121-chr2:48771521..48774088,2	K562	blood:
3	chr2:48666517..48672497-chr2:48674609..48679967,9	MCF-7	breast:
4	chr2:48667785..48669496-chr2:48677557..48679118,2	K562	blood:

Variant related genes	Relation type
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10185212	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10865229	0.89[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12477901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13386132	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3811520	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs4328683	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4371401	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4429520	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4430989	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4464333	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953574	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953585	1.00[EUR][1000 genomes]
rs4953588	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953590	0.87[EUR][1000 genomes]
rs60578339	1.00[AMR][1000 genomes]
rs6545040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545043	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6545044	1.00[CEU][hapmap]
rs6715766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6756820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7355307	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs7557764	1.00[EUR][1000 genomes]
rs7577850	0.89[CHB][hapmap];0.88[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];1.00[YRI][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48668600-48682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48668800-48678800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:48668800-48679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr2:48668800-48682400	Weak transcription	Lung	lung
5	chr2:48669000-48678800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr2:48669000-48679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:48669000-48680000	Weak transcription	Fetal Stomach	stomach
8	chr2:48669000-48681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:48669000-48683400	Weak transcription	Right Ventricle	heart
10	chr2:48669200-48698200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:48669400-48685000	Weak transcription	Fetal Brain Female	brain
12	chr2:48669400-48693800	Weak transcription	Hela-S3	cervix
13	chr2:48669600-48694200	Weak transcription	Fetal Brain Male	brain
14	chr2:48670000-48679000	Weak transcription	Brain Germinal Matrix	brain
15	chr2:48670400-48678800	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:48670400-48678800	Weak transcription	Ovary	ovary
17	chr2:48670800-48681800	Weak transcription	Gastric	stomach
18	chr2:48670800-48681800	Weak transcription	Spleen	Spleen
19	chr2:48671600-48681800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:48671800-48692400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:48673000-48679000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:48673000-48681600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:48673000-48681800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr2:48673000-48682000	Weak transcription	Esophagus	oesophagus
25	chr2:48673000-48686800	Weak transcription	Pancreas	Pancrea
26	chr2:48673000-48697400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:48673200-48679200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:48673600-48679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:48673600-48679000	Weak transcription	Left Ventricle	heart
31	chr2:48674200-48679200	Enhancers	K562	blood
32	chr2:48674800-48678800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr2:48674800-48687000	Weak transcription	Small Intestine	intestine
34	chr2:48675200-48678800	Enhancers	Brain Substantia Nigra	brain
35	chr2:48675200-48679400	Enhancers	HSMMtube	muscle
36	chr2:48675200-48679600	Enhancers	Liver	Liver
37	chr2:48675200-48679600	Enhancers	Placenta Amnion	Placenta Amnion
38	chr2:48675200-48680000	Enhancers	Brain Cingulate Gyrus	brain
39	chr2:48675200-48680400	Enhancers	Brain Anterior Caudate	brain
40	chr2:48675600-48679000	Enhancers	Brain Angular Gyrus	brain
41	chr2:48675800-48681800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:48675800-48687800	Weak transcription	Fetal Kidney	kidney
43	chr2:48676000-48679000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:48676000-48679000	Weak transcription	NHLF	lung
45	chr2:48676000-48679600	Enhancers	Fetal Heart	heart
46	chr2:48676000-48681800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:48676200-48678800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:48676200-48679000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr2:48676200-48679000	Weak transcription	Thymus	Thymus
50	chr2:48676200-48679400	Enhancers	Pancreatic Islets	Pancreatic Islet

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