Variant report

Variant	rs12906497
Chromosome Location	chr15:43030660-43030661
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	chr15:43029256..43031403-chr15:43210732..43214178,4	K562	blood:
2	chr15:43014319..43018768-chr15:43027782..43030873,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140326	Chromatin interaction
ENSG00000128881	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10162939	0.82[CEU][hapmap]
rs10400824	0.82[EUR][1000 genomes]
rs11070374	1.00[YRI][hapmap]
rs1197550	0.82[CEU][hapmap]
rs1197551	0.82[CEU][hapmap]
rs12102055	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12594483	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs12594855	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12905385	0.85[CEU][hapmap]
rs12905592	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12907826	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12912064	0.89[EUR][1000 genomes]
rs12914570	0.80[CEU][hapmap]
rs12917018	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12917189	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957020	0.83[EUR][1000 genomes]
rs16957091	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957104	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1705356	0.80[CEU][hapmap]
rs1915241	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995939	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136899	0.80[CEU][hapmap]
rs2136900	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2136901	0.90[ASN][1000 genomes]
rs2280048	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305084	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2305085	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2412740	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2412741	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28479391	0.85[ASN][1000 genomes]
rs28549876	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28562951	0.89[EUR][1000 genomes]
rs28798437	0.82[EUR][1000 genomes]
rs28811114	0.81[EUR][1000 genomes]
rs28823029	0.81[EUR][1000 genomes]
rs3099758	0.80[CEU][hapmap]
rs3199486	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34191150	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35616173	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs35738819	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3742987	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742988	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4265781	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923950	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4924690	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4924691	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs4994112	0.90[CEU][hapmap];0.81[CHB][hapmap]
rs623271	0.80[CEU][hapmap]
rs6493059	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs6493060	0.85[CHB][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs6493061	0.85[CHB][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs6493062	0.81[EUR][1000 genomes]
rs6493063	0.95[EUR][1000 genomes]
rs6493066	0.84[EUR][1000 genomes]
rs6493067	1.00[YRI][hapmap]
rs6493068	1.00[YRI][hapmap]
rs66681258	0.82[EUR][1000 genomes]
rs67391479	0.87[EUR][1000 genomes]
rs7163030	0.87[EUR][1000 genomes]
rs7166373	0.80[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7166632	0.85[EUR][1000 genomes]
rs7166775	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7167392	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7167802	1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap]
rs7169009	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169202	0.89[CHB][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7174041	0.85[CEU][hapmap];0.89[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175582	0.80[CEU][hapmap];0.92[EUR][1000 genomes]
rs7182141	0.80[CEU][hapmap];0.91[EUR][1000 genomes]
rs7182753	1.00[YRI][hapmap]
rs731984	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023524	0.86[CEU][hapmap]
rs8026233	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027427	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030587	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs8034447	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034664	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8043472	0.80[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9269	0.90[CEU][hapmap];0.92[EUR][1000 genomes]
rs9783683	1.00[YRI][hapmap]
rs9783713	0.92[EUR][1000 genomes]
rs9919994	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs9920163	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9944248	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43029400-43051200	Weak transcription	Spleen	Spleen
2	chr15:43029600-43045000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:43029800-43030800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:43029800-43037800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr15:43029800-43037800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:43029800-43037800	Weak transcription	Fetal Stomach	stomach
7	chr15:43029800-43037800	Weak transcription	Lung	lung
8	chr15:43029800-43037800	Weak transcription	Ovary	ovary
9	chr15:43029800-43041400	Weak transcription	Psoas Muscle	Psoas
10	chr15:43029800-43043200	Weak transcription	Left Ventricle	heart
11	chr15:43029800-43043800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:43029800-43044000	Weak transcription	Right Ventricle	heart
13	chr15:43029800-43044200	Weak transcription	Fetal Brain Male	brain
14	chr15:43029800-43047600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr15:43029800-43047800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:43029800-43050800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr15:43029800-43051200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:43029800-43051200	Weak transcription	Esophagus	oesophagus
19	chr15:43029800-43051200	Weak transcription	Gastric	stomach
20	chr15:43029800-43051400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:43029800-43071000	Weak transcription	Pancreas	Pancrea
22	chr15:43030000-43032800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:43030000-43033000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:43030000-43033200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr15:43030000-43034600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:43030000-43035400	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr15:43030000-43035600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:43030000-43035600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:43030000-43036200	Weak transcription	Adipose Nuclei	Adipose
30	chr15:43030000-43036400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:43030000-43036400	Weak transcription	Primary hematopoietic stem cells	blood
32	chr15:43030000-43036400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr15:43030000-43036400	Weak transcription	Brain Substantia Nigra	brain
34	chr15:43030000-43036400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:43030000-43036600	Weak transcription	Placenta	Placenta
36	chr15:43030000-43036600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr15:43030000-43037200	Weak transcription	NH-A	brain
38	chr15:43030000-43037400	Weak transcription	Primary B cells from cord blood	blood
39	chr15:43030000-43037600	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:43030000-43037600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:43030000-43037600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:43030000-43037800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:43030000-43037800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:43030000-43037800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:43030000-43037800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr15:43030000-43037800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:43030000-43037800	Weak transcription	Brain Angular Gyrus	brain
48	chr15:43030000-43037800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:43030000-43037800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:43030000-43037800	Weak transcription	HUVEC	blood vessel

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