Variant report

Variant	rs12564279
Chromosome Location	chr1:171477355-171477356
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:171477145-171477418	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171476110..171477737-chr1:171479452..171480963,2	MCF-7	breast:

Variant related genes	Relation type
PRRC2C	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10913017	0.83[AFR][1000 genomes]
rs10913119	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10913149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913197	1.00[YRI][hapmap]
rs10913285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913292	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12076841	0.83[AFR][1000 genomes]
rs12080096	1.00[YRI][hapmap]
rs12562424	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12567152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038040	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2038041	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2038043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2179882	0.92[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2294291	1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs3204333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57562814	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60014783	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6676140	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6681173	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6702038	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72717832	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72717839	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72717840	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72717853	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72717854	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7517178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522026	0.85[AMR][1000 genomes];0.82[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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
2	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
4	chr1:171457800-171482000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:171457800-171482200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:171459000-171482000	Weak transcription	HMEC	breast
7	chr1:171460800-171481400	Weak transcription	HSMM	muscle
8	chr1:171462600-171478000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:171462600-171482400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:171463000-171483200	Weak transcription	Fetal Muscle Leg	muscle
11	chr1:171464000-171483200	Weak transcription	Esophagus	oesophagus
12	chr1:171464200-171481600	Weak transcription	NHEK	skin
13	chr1:171465200-171481800	Weak transcription	HUVEC	blood vessel
14	chr1:171465200-171482200	Weak transcription	Fetal Lung	lung
15	chr1:171465200-171483200	Weak transcription	NHLF	lung
16	chr1:171465200-171483600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:171468000-171482200	Weak transcription	Hela-S3	cervix
18	chr1:171468400-171483200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:171468800-171483600	Weak transcription	Gastric	stomach
20	chr1:171469000-171483600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:171469400-171481400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:171469600-171482200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:171470200-171481200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:171470200-171481600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:171470200-171482800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr1:171470600-171482200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:171470600-171483600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:171470600-171491600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:171470800-171481400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr1:171470800-171482200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr1:171471400-171483200	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:171471400-171485800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:171471600-171483200	Weak transcription	Fetal Brain Female	brain
34	chr1:171471600-171483600	Weak transcription	Brain Germinal Matrix	brain
35	chr1:171471600-171483600	Weak transcription	Fetal Brain Male	brain
36	chr1:171472000-171480600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr1:171472000-171481200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:171472000-171483800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:171472200-171478400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:171472200-171481000	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr1:171472400-171481600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:171472400-171482200	Weak transcription	Fetal Thymus	thymus
43	chr1:171472400-171483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:171472400-171483600	Weak transcription	Aorta	Aorta
45	chr1:171472600-171478200	Weak transcription	Fetal Intestine Small	intestine
46	chr1:171472600-171481800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:171472600-171483200	Weak transcription	Lung	lung
48	chr1:171472600-171483800	Weak transcription	Fetal Stomach	stomach
49	chr1:171473000-171479800	Enhancers	Primary T cells from cord blood	blood
50	chr1:171473000-171481400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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