Variant report

Variant	rs7612599
Chromosome Location	chr3:56647934-56647935
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	POLR2A	chr3:56647833-56648034	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:56647824-56647955	ProgFib	skin:	n/a	n/a
3	POLR2A	chr3:56647783-56647983	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56647300..56648856-chr3:56648916..56651486,2	K562	blood:

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10212341	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1045926	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865998	0.82[ASN][1000 genomes]
rs10865999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10866000	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130538	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11706624	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11714608	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11714897	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11715395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719656	0.87[ASN][1000 genomes]
rs11921326	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488218	0.87[ASN][1000 genomes]
rs12490749	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493637	0.81[ASN][1000 genomes]
rs12636773	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12715490	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13094666	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13097030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13097288	0.86[ASN][1000 genomes]
rs1352766	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1491166	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs17056878	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17216740	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2004199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029465	0.82[ASN][1000 genomes]
rs2035798	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2054987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2054988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2291499	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317133	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];1.00[ASN][1000 genomes]
rs2317245	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs282533	0.81[CHB][hapmap]
rs35998149	0.82[ASN][1000 genomes]
rs3732512	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4093514	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4681746	0.95[CHB][hapmap];0.96[JPT][hapmap]
rs4681951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4974220	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4974224	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57800049	0.82[AMR][1000 genomes]
rs6445805	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6445806	0.80[AMR][1000 genomes]
rs66529035	0.87[ASN][1000 genomes]
rs6765870	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6774323	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6784100	0.81[ASN][1000 genomes]
rs6785479	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798118	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6799576	0.87[ASN][1000 genomes]
rs6802051	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6804262	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6805469	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72877266	0.85[ASN][1000 genomes]
rs7432897	0.81[ASN][1000 genomes]
rs7618024	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7626378	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629559	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811046	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9820759	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9840528	0.95[CEU][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9842283	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9845096	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845655	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9846282	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9858728	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9862490	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9881005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9881154	0.92[ASN][1000 genomes]
rs9881789	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9881961	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985253	1.00[CEU][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9985254	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56629000-56648000	Weak transcription	NH-A	brain
9	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
10	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
12	chr3:56640000-56650000	Weak transcription	HMEC	breast
13	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
14	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:56640800-56649400	Weak transcription	Osteobl	bone
18	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
19	chr3:56640800-56650400	Weak transcription	NHLF	lung
20	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
21	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
26	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
28	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:56644800-56648200	Strong transcription	Fetal Stomach	stomach
33	chr3:56644800-56648400	Strong transcription	Primary B cells from peripheral blood	blood
34	chr3:56644800-56648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:56644800-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:56644800-56649600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
39	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr3:56645000-56648200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:56645000-56650600	Weak transcription	A549	lung
43	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:56645400-56648000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:56645400-56653800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:56645400-56667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr3:56645400-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr3:56645600-56648000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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