Variant report

Variant	rs12619486
Chromosome Location	chr2:55516103-55516104
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55512725..55515035-chr2:55515151..55518093,2	MCF-7	breast:
2	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
3	chr2:55514301..55516151-chr2:55518959..55520928,3	MCF-7	breast:
4	chr2:55516061..55518491-chr2:55518529..55520349,2	K562	blood:

Variant related genes	Relation type
ENSG00000206964	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10188143	1.00[JPT][hapmap]
rs10496038	1.00[MEX][hapmap]
rs11686912	1.00[MEX][hapmap]
rs12623460	1.00[EUR][1000 genomes]
rs12623872	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs13032294	1.00[MEX][hapmap]
rs2589074	1.00[EUR][1000 genomes]
rs28364599	0.85[AMR][1000 genomes]
rs35183885	1.00[MEX][hapmap]
rs6742306	1.00[MEX][hapmap]
rs7558675	1.00[EUR][1000 genomes]
rs7595814	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv1799450	chr2:55494904-55520842	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
5	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55501000-55517000	Weak transcription	Hela-S3	cervix
2	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:55509800-55518600	Weak transcription	HMEC	breast
6	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:55510000-55516200	Weak transcription	Fetal Lung	lung
8	chr2:55510000-55518800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
13	chr2:55510000-55521800	Weak transcription	NHEK	skin
14	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
21	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:55510200-55516200	Weak transcription	NHDF-Ad	bronchial
24	chr2:55510200-55516600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:55510200-55517400	Weak transcription	Fetal Brain Female	brain
26	chr2:55510200-55519200	Weak transcription	Ovary	ovary
27	chr2:55510200-55520600	Weak transcription	HSMMtube	muscle
28	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
29	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:55510200-55522400	Weak transcription	NHLF	lung
32	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
33	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
34	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
35	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
36	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
37	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
38	chr2:55510600-55519400	Weak transcription	Primary B cells from cord blood	blood
39	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:55510600-55522400	Weak transcription	A549	lung
41	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
42	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr2:55510600-55537400	Weak transcription	Lung	lung
44	chr2:55510800-55518200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:55510800-55518600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:55510800-55521200	Weak transcription	Osteobl	bone
47	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr2:55511000-55518800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:55511000-55519600	Weak transcription	Primary T cells fromperipheralblood	blood

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