Variant report

Variant	rs12540517
Chromosome Location	chr7:129519022-129519023
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:129516554..129519398-chr7:129644770..129647291,2	K562	blood:
2	chr7:129516752..129519890-chr7:129589856..129592856,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186591	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs12530557	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531622	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531936	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532612	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532959	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533033	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533290	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533464	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12533528	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533953	0.86[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534061	1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534320	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535347	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535722	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535728	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535857	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536978	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537150	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537336	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537576	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537604	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537660	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537782	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538787	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539145	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539653	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539800	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540541	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1464970	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471874	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471877	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559301	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965567	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1965568	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2727457	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930431	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35189138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55675451	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732825	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55735840	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55748031	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55767113	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55769831	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772531	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798026	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809128	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56022754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025626	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034137	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080853	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085705	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56094908	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117230	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153730	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167610	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176516	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56191413	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321762	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332361	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333543	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56376893	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56381627	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56408895	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718925	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718926	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][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	nsv533849	chr7:129462947-129616625	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129475000-129534800	Weak transcription	Colonic Mucosa	Colon
2	chr7:129479400-129543600	Weak transcription	Thymus	Thymus
3	chr7:129496400-129520400	Weak transcription	Fetal Brain Female	brain
4	chr7:129497000-129536800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:129503200-129519800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr7:129503200-129529000	Weak transcription	Gastric	stomach
7	chr7:129503400-129538400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:129504200-129519200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr7:129505600-129529600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:129505600-129545600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:129506000-129542800	Weak transcription	Small Intestine	intestine
12	chr7:129506800-129519600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr7:129506800-129520600	Weak transcription	Fetal Kidney	kidney
14	chr7:129509600-129541000	Weak transcription	Spleen	Spleen
15	chr7:129510200-129524600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:129510600-129541000	Weak transcription	Esophagus	oesophagus
17	chr7:129511200-129529000	Weak transcription	Brain Germinal Matrix	brain
18	chr7:129511200-129529600	Weak transcription	Brain Substantia Nigra	brain
19	chr7:129512000-129520000	Weak transcription	Dnd41	blood
20	chr7:129512000-129524400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:129512000-129529600	Weak transcription	Fetal Stomach	stomach
22	chr7:129513200-129548600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr7:129513400-129519200	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:129513800-129529600	Weak transcription	Fetal Intestine Small	intestine
25	chr7:129515200-129520000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr7:129515600-129519600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:129515600-129519800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr7:129515600-129520000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
29	chr7:129515600-129520800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:129515600-129521000	Strong transcription	Primary B cells from peripheral blood	blood
31	chr7:129515600-129521000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr7:129515600-129521000	Strong transcription	GM12878-XiMat	blood
33	chr7:129515800-129519200	Strong transcription	Fetal Thymus	thymus
34	chr7:129515800-129519400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr7:129515800-129520800	Strong transcription	Placenta	Placenta
36	chr7:129515800-129521800	Strong transcription	Primary B cells from cord blood	blood
37	chr7:129516000-129519400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr7:129516000-129529400	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr7:129516200-129520200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:129516200-129521600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:129516200-129521800	Weak transcription	NHDF-Ad	bronchial
42	chr7:129516200-129525400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:129516200-129526000	Weak transcription	NHLF	lung
44	chr7:129516200-129526200	Weak transcription	Ovary	ovary
45	chr7:129516200-129529000	Weak transcription	Aorta	Aorta
46	chr7:129516200-129529000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr7:129516200-129542800	Weak transcription	HSMMtube	muscle
48	chr7:129516200-129584400	Weak transcription	Fetal Brain Male	brain
49	chr7:129516400-129528000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr7:129516600-129528800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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