Variant report

Variant	rs17223377
Chromosome Location	chr12:65062388-65062389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:65060197..65063075-chr12:65066604..65068445,2	K562	blood:
2	chr12:65004967..65007120-chr12:65061292..65063041,2	K562	blood:
3	chr12:65061393..65063543-chr12:65063755..65066081,2	MCF-7	breast:
4	chr12:65057089..65063734-chr12:65063788..65069344,8	K562	blood:
5	chr12:64844874..64846607-chr12:65061898..65064676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183735	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008159	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1008160	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175470	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11175476	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175478	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11175481	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175497	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175509	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11837759	0.85[CEU][hapmap]
rs12230536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12814316	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816847	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12824246	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12829878	0.85[CEU][hapmap]
rs12830436	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12831875	0.85[CEU][hapmap]
rs12833931	0.87[EUR][1000 genomes]
rs17223244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17223391	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17823442	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2078398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35512928	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35674528	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35705715	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35860561	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7303641	0.82[EUR][1000 genomes]
rs7304648	0.82[EUR][1000 genomes]
rs7959471	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65047800-65063000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:65048000-65063000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr12:65057200-65063000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:65057800-65063200	Enhancers	Primary B cells from peripheral blood	blood
5	chr12:65058200-65062600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:65058200-65062600	Enhancers	Psoas Muscle	Psoas
7	chr12:65058200-65064400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:65058400-65063000	Enhancers	Primary B cells from cord blood	blood
9	chr12:65058400-65069600	Enhancers	Small Intestine	intestine
10	chr12:65058800-65062400	Enhancers	Right Atrium	heart
11	chr12:65058800-65063000	Enhancers	HepG2	liver
12	chr12:65058800-65063200	Enhancers	K562	blood
13	chr12:65058800-65066600	Enhancers	Stomach Mucosa	stomach
14	chr12:65058800-65070000	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr12:65059000-65063000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr12:65059000-65063000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:65059000-65065800	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr12:65059200-65062600	Enhancers	Left Ventricle	heart
19	chr12:65059200-65062600	Enhancers	Lung	lung
20	chr12:65059200-65063000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr12:65059400-65062400	Enhancers	Colonic Mucosa	Colon
22	chr12:65059400-65062600	Enhancers	Pancreas	Pancrea
23	chr12:65059400-65063000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr12:65059400-65063000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:65059400-65065200	Enhancers	H1 Cell Line	embryonic stem cell
26	chr12:65059400-65066000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr12:65059400-65068800	Enhancers	Fetal Intestine Large	intestine
28	chr12:65059600-65062800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr12:65059600-65063000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr12:65059600-65063000	Enhancers	Fetal Thymus	thymus
31	chr12:65059600-65064600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:65059800-65062400	Enhancers	Fetal Lung	lung
33	chr12:65059800-65062800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr12:65059800-65062800	Weak transcription	HMEC	breast
35	chr12:65059800-65063000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:65059800-65063000	Weak transcription	Brain Substantia Nigra	brain
37	chr12:65059800-65063000	Weak transcription	HSMM	muscle
38	chr12:65060000-65062800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:65060000-65063000	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr12:65060000-65063000	Enhancers	HUVEC	blood vessel
41	chr12:65060000-65073400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr12:65060200-65069200	Weak transcription	Osteobl	bone
43	chr12:65060400-65062400	Enhancers	Placenta	Placenta
44	chr12:65060400-65062400	Enhancers	Gastric	stomach
45	chr12:65060400-65063000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr12:65060400-65065600	Enhancers	Spleen	Spleen
47	chr12:65060600-65062600	Weak transcription	Thymus	Thymus
48	chr12:65060600-65062800	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr12:65060600-65062800	Enhancers	A549	lung
50	chr12:65060600-65063000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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