Variant report

Variant	rs924050
Chromosome Location	chr12:26163996-26163997
allele	G/T
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	STAT3	chr12:26163968-26164627	MCF10A-Er-Src	breast:	n/a	chr12:26164305-26164313 chr12:26164380-26164388 chr12:26164303-26164314 chr12:26164280-26164291
2	CTCF	chr12:26163860-26164010	AoAF	blood vessel:	n/a	n/a
3	PBX3	chr12:26163075-26164580	SK-N-SH	brain:	n/a	n/a
4	CTCF	chr12:26163940-26164090	AG09319	gingival:	n/a	n/a
5	CTCF	chr12:26163940-26164090	AG10803	skin:	n/a	n/a
6	GATA3	chr12:26163041-26164553	SK-N-SH	brain:	n/a	chr12:26163567-26163574 chr12:26163798-26163809 chr12:26164176-26164185
7	CTCF	chr12:26163920-26164070	BJ	skin:	n/a	n/a
8	FOS	chr12:26163960-26164547	MCF10A-Er-Src	breast:	n/a	chr12:26164174-26164184 chr12:26164174-26164184 chr12:26164174-26164184 chr12:26164174-26164184
9	STAT3	chr12:26163902-26164547	MCF10A-Er-Src	breast:	n/a	chr12:26164305-26164313 chr12:26164380-26164388 chr12:26164303-26164314 chr12:26164280-26164291
10	TCF12	chr12:26163053-26164648	SK-N-SH	brain:	n/a	n/a
11	TCF12	chr12:26163044-26164692	SK-N-SH	brain:	n/a	n/a
12	GATA3	chr12:26162988-26164584	SK-N-SH	brain:	n/a	chr12:26163567-26163574 chr12:26163798-26163809 chr12:26164176-26164185
13	FOS	chr12:26163982-26164547	MCF10A-Er-Src	breast:	n/a	chr12:26164174-26164184 chr12:26164174-26164184 chr12:26164174-26164184 chr12:26164174-26164184
14	EP300	chr12:26163004-26164496	SK-N-SH	brain:	n/a	chr12:26163325-26163334

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:26115121..26117506-chr12:26161572..26164104,2	MCF-7	breast:

Variant related genes	Relation type
RASSF8	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1069974	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732539	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10842657	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11048399	1.00[JPT][hapmap]
rs1167537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1390323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390325	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1472322	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1495654	0.92[EUR][1000 genomes]
rs1495656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1495661	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1513125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1979748	0.87[ASN][1000 genomes]
rs1994996	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994998	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2055181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246596	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2634179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2643937	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2643938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2669555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729645	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2729651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2729661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2729662	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803007	1.00[CEU][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56306595	0.87[ASN][1000 genomes]
rs706522	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs706528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7972703	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];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980111	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs829983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829986	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863807	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs864920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs924051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26160600-26167000	Weak transcription	Gastric	stomach
2	chr12:26160600-26168000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:26160600-26168200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr12:26160600-26168200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr12:26160600-26168200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr12:26160600-26170400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:26160600-26170600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:26160600-26171600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:26161400-26164800	Enhancers	Rectal Smooth Muscle	rectum
10	chr12:26161600-26164200	Enhancers	Fetal Heart	heart
11	chr12:26161600-26164600	Enhancers	Brain Anterior Caudate	brain
12	chr12:26161600-26167400	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr12:26161800-26164800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:26161800-26164800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:26161800-26164800	Enhancers	Right Atrium	heart
16	chr12:26161800-26165000	Enhancers	Colon Smooth Muscle	Colon
17	chr12:26162000-26164800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr12:26162200-26164000	Weak transcription	Fetal Lung	lung
19	chr12:26162400-26164600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:26162400-26164600	Enhancers	Brain Substantia Nigra	brain
21	chr12:26162400-26164800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:26162400-26164800	Enhancers	Left Ventricle	heart
23	chr12:26162400-26164800	Enhancers	Ovary	ovary
24	chr12:26162400-26164800	Enhancers	Psoas Muscle	Psoas
25	chr12:26162400-26165000	Enhancers	HUVEC	blood vessel
26	chr12:26162600-26164000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:26162600-26164200	Enhancers	Brain Angular Gyrus	brain
28	chr12:26162600-26164400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:26162600-26164800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:26162600-26164800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:26162600-26164800	Enhancers	Adipose Nuclei	Adipose
32	chr12:26162600-26164800	Enhancers	HMEC	breast
33	chr12:26162600-26164800	Enhancers	NHEK	skin
34	chr12:26162600-26164800	Enhancers	NHLF	lung
35	chr12:26162600-26165200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr12:26162800-26164200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:26162800-26164600	Enhancers	NH-A	brain
38	chr12:26162800-26164800	Enhancers	HSMM	muscle
39	chr12:26163000-26164200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:26163000-26164200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr12:26163000-26164400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:26163000-26164800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr12:26163000-26164800	Enhancers	Fetal Muscle Leg	muscle
44	chr12:26163000-26164800	Enhancers	Right Ventricle	heart
45	chr12:26163200-26164200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr12:26163200-26164200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:26163200-26164800	Enhancers	Brain Hippocampus Middle	brain
48	chr12:26163200-26164800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr12:26163200-26164800	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr12:26163200-26165200	Enhancers	NHDF-Ad	bronchial

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