Variant report

Variant	rs12690
Chromosome Location	chr7:129470961-129470962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:129469301..129471027-chr7:129477016..129479280,2	MCF-7	breast:
2	chr7:129469764..129472674-chr7:129485963..129488214,2	K562	blood:
3	chr7:129469744..129473001-chr7:129646960..129649932,3	K562	blood:
4	chr7:129249214..129251582-chr7:129470289..129473401,3	K562	blood:
5	chr7:129469886..129472381-chr7:129587283..129590699,3	MCF-7	breast:
6	chr7:129468198..129471142-chr7:129597545..129600356,2	MCF-7	breast:
7	chr7:129468043..129473404-chr7:129589451..129593815,6	MCF-7	breast:
8	chr7:129470312..129471900-chr7:129537078..129538662,2	K562	blood:
9	chr7:129464031..129466452-chr7:129468201..129471315,4	MCF-7	breast:
10	chr7:129463253..129467439-chr7:129470010..129474375,4	K562	blood:
11	chr7:129468911..129471466-chr7:129477824..129480519,2	MCF-7	breast:
12	chr7:129419635..129422610-chr7:129468261..129471456,4	MCF-7	breast:
13	chr7:129470865..129472484-chr7:129587803..129590371,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3HC1-4	chr7:129470575-129472418	NONHSAT123314

No data

Variant related genes	Relation type
ENSG00000186591	Chromatin interaction
ENSG00000106459	Chromatin interaction
ENSG00000244036	Chromatin interaction
ENSG00000273329	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	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531622	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12531936	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532612	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533290	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533464	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12533528	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12533953	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12534043	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534061	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535347	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12535722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535857	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12536424	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537150	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537604	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12537660	1.00[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]
rs12537782	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538787	1.00[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]
rs12539145	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539653	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12539800	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540479	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12540517	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]
rs12540541	1.00[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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1464972	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1471874	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1471877	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559301	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965567	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1965568	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2631601	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2727457	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34930431	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35189138	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55675451	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55732825	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55735840	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55748031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55767113	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55769831	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55772531	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55809128	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56022754	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56025626	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56034137	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56080853	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56085705	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56094908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117230	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56153730	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167610	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56176516	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56191413	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56321762	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56332361	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56333543	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56376893	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56381627	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56408895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718925	1.00[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]
rs718926	1.00[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]
rs7639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:129466000-129471200	Weak transcription	Primary T cells from cord blood	blood
2	chr7:129466000-129471600	Weak transcription	Thymus	Thymus
3	chr7:129466200-129475200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr7:129466200-129483800	Weak transcription	Dnd41	blood
5	chr7:129466400-129483400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr7:129467000-129471200	Weak transcription	Hela-S3	cervix
7	chr7:129468200-129472000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:129468800-129471200	Enhancers	Fetal Muscle Leg	muscle
9	chr7:129468800-129472200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr7:129468800-129472200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr7:129469000-129472000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:129469000-129472400	Enhancers	Right Ventricle	heart
13	chr7:129469200-129472000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:129469400-129471600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:129469400-129471800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr7:129469400-129471800	Enhancers	HSMM	muscle
17	chr7:129469400-129472400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr7:129469600-129471000	Enhancers	Spleen	Spleen
19	chr7:129469600-129472000	Enhancers	Pancreas	Pancrea
20	chr7:129469600-129472600	Enhancers	Left Ventricle	heart
21	chr7:129469600-129473000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr7:129469800-129471800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr7:129469800-129471800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:129469800-129471800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr7:129469800-129472000	Enhancers	Placenta	Placenta
26	chr7:129469800-129472400	Enhancers	Aorta	Aorta
27	chr7:129470000-129471000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr7:129470000-129471400	Flanking Active TSS	NH-A	brain
29	chr7:129470000-129472200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr7:129470000-129480400	Weak transcription	Fetal Brain Male	brain
31	chr7:129470200-129471400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:129470200-129471800	Enhancers	HSMMtube	muscle
33	chr7:129470200-129472400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr7:129470400-129471000	Enhancers	Brain Anterior Caudate	brain
35	chr7:129470400-129471000	Enhancers	Esophagus	oesophagus
36	chr7:129470400-129471000	Enhancers	Fetal Lung	lung
37	chr7:129470400-129471200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:129470400-129471200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:129470400-129471200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:129470400-129471400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr7:129470400-129471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr7:129470400-129471400	Weak transcription	Colonic Mucosa	Colon
43	chr7:129470400-129471400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:129470400-129471400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr7:129470400-129471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr7:129470400-129471600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr7:129470400-129471600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:129470400-129471600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr7:129470400-129471600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr7:129470400-129471600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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