Variant report

Variant	rs12039417
Chromosome Location	chr1:77685937-77685938
allele	C/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	IRF1	chr1:77685750-77686109	K562	blood:	n/a	n/a
2	HCFC1	chr1:77683952-77686153	Hela-S3	cervix:	n/a	n/a
3	MXI1	chr1:77683938-77686114	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
PIGK	TF binding region
ENSG00000154027	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1028737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10782640	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11162271	0.96[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs1146673	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146674	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1146675	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[ASN][1000 genomes]
rs11806823	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs12032956	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12093471	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1253217	0.96[ASN][1000 genomes]
rs1253225	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562725	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1270496	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1314045	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169216	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1779188	0.96[ASN][1000 genomes]
rs199710	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs199711	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs199715	0.90[ASN][1000 genomes]
rs2051127	0.98[ASN][1000 genomes]
rs2069224	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[ASN][1000 genomes]
rs2134351	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4399204	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4443938	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4509622	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949649	0.82[ASN][1000 genomes]
rs4949766	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs4949767	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949771	0.91[ASN][1000 genomes]
rs6603934	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6603936	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6668949	0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs713232	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71592399	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7417698	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7522008	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7524151	0.92[ASN][1000 genomes]
rs7525056	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535408	0.92[ASN][1000 genomes]
rs7538430	0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[ASN][1000 genomes]
rs7543898	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs940282	0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr1:77682800-77686400	Active TSS	GM12878-XiMat	blood
2	chr1:77683600-77686200	Active TSS	K562	blood
3	chr1:77683800-77686000	Active TSS	NHLF	lung
4	chr1:77683800-77686200	Active TSS	A549	lung
5	chr1:77684000-77686000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:77684000-77686000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:77684000-77686000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:77684000-77686000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:77684000-77686000	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:77684000-77686000	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr1:77684000-77686000	Active TSS	Thymus	Thymus
12	chr1:77684000-77686200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:77684000-77686200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:77684000-77686200	Active TSS	NHDF-Ad	bronchial
16	chr1:77684000-77686600	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr1:77684200-77686000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:77684200-77686000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:77684200-77686000	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr1:77684200-77686000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:77684200-77686000	Active TSS	Brain Germinal Matrix	brain
22	chr1:77684200-77686000	Active TSS	Fetal Intestine Large	intestine
23	chr1:77684200-77686000	Active TSS	Fetal Intestine Small	intestine
24	chr1:77684200-77686000	Active TSS	Fetal Kidney	kidney
25	chr1:77684200-77686000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr1:77684200-77686000	Active TSS	Fetal Muscle Leg	muscle
27	chr1:77684200-77686000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr1:77684200-77686000	Active TSS	Stomach Smooth Muscle	stomach
29	chr1:77684200-77686200	Active TSS	HMEC	breast
30	chr1:77684200-77686400	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr1:77684200-77686400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:77684400-77686000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:77684400-77686000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:77684400-77686000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:77684400-77686000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:77684400-77686000	Active TSS	Brain Cingulate Gyrus	brain
37	chr1:77684400-77686000	Active TSS	Fetal Brain Female	brain
38	chr1:77684400-77686000	Active TSS	Fetal Muscle Trunk	muscle
39	chr1:77684400-77686000	Active TSS	Right Ventricle	heart
40	chr1:77684400-77686000	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr1:77684400-77686200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:77684600-77686000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:77684600-77686000	Active TSS	Rectal Mucosa Donor 31	rectum
44	chr1:77684600-77686000	Active TSS	HSMM	muscle
45	chr1:77684600-77686200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:77684600-77686800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:77685200-77687000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:77685200-77687800	Weak transcription	Spleen	Spleen
49	chr1:77685400-77686000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:77685400-77686200	Flanking Active TSS	Primary T cells from cord blood	blood

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