Variant report

Variant	rs12540484
Chromosome Location	chr7:127370040-127370041
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:127364711..127367506-chr7:127369720..127371248,2	MCF-7	breast:
2	chr7:127363061..127365825-chr7:127368280..127370347,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10954164	0.85[ASN][1000 genomes]
rs11768841	0.81[ASN][1000 genomes]
rs11772303	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12539411	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12667197	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12668077	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12672945	0.80[ASN][1000 genomes]
rs12673293	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1419967	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16871926	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17151229	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17151377	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17151470	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2058457	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2402871	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3757778	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757780	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3808078	0.81[AMR][1000 genomes]
rs3808086	0.84[ASN][1000 genomes]
rs3808088	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3824003	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4728079	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4731377	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56185520	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58106688	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59140894	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62481385	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62481416	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481419	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62481443	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs62481447	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62481450	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs67338333	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs698408	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712707	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs712715	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs712718	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs712719	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765971	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs806166	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs806169	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs806172	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs806174	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs806188	0.94[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs882694	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791922	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1031658	chr7:127266882-127376775	Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv831123	chr7:127289511-127510396	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1030387	chr7:127348973-127455890	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127324800-127372200	Weak transcription	Fetal Heart	heart
2	chr7:127326600-127379800	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr7:127326800-127371000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:127331600-127375600	Strong transcription	Fetal Thymus	thymus
5	chr7:127334400-127376600	Weak transcription	Fetal Brain Male	brain
6	chr7:127339400-127371000	Weak transcription	Right Atrium	heart
7	chr7:127344600-127371200	Weak transcription	Brain Germinal Matrix	brain
8	chr7:127347800-127383000	Strong transcription	NHEK	skin
9	chr7:127349600-127371200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:127351400-127375600	Strong transcription	Liver	Liver
11	chr7:127351400-127383800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr7:127351600-127382200	Strong transcription	K562	blood
13	chr7:127351800-127371000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr7:127352200-127372400	Strong transcription	HepG2	liver
15	chr7:127352600-127375600	Strong transcription	Primary T cells from cord blood	blood
16	chr7:127352800-127370400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr7:127354000-127370400	Weak transcription	Brain Angular Gyrus	brain
18	chr7:127354200-127370600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:127354200-127374000	Weak transcription	Fetal Brain Female	brain
20	chr7:127354200-127376600	Weak transcription	Psoas Muscle	Psoas
21	chr7:127354400-127370400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:127354400-127370600	Weak transcription	Fetal Kidney	kidney
23	chr7:127355200-127380000	Strong transcription	GM12878-XiMat	blood
24	chr7:127356600-127375600	Strong transcription	Primary B cells from cord blood	blood
25	chr7:127357200-127375200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:127357200-127382600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:127357400-127375000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr7:127357400-127375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:127357400-127380800	Strong transcription	Fetal Intestine Large	intestine
30	chr7:127357600-127375200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:127357600-127375400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:127357600-127387000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:127357800-127378200	Strong transcription	Primary T helper cells PMA-I stimulated	--
34	chr7:127358000-127373000	Strong transcription	NH-A	brain
35	chr7:127358200-127370400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:127358200-127370800	Weak transcription	Fetal Lung	lung
37	chr7:127358200-127374800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:127358800-127370400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:127358800-127371000	Weak transcription	Esophagus	oesophagus
40	chr7:127358800-127371000	Weak transcription	Spleen	Spleen
41	chr7:127359600-127370600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:127359800-127375400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:127360000-127377800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr7:127360000-127379200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr7:127360400-127374800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:127360600-127370600	Weak transcription	Brain Substantia Nigra	brain
47	chr7:127360600-127371200	Weak transcription	Brain Anterior Caudate	brain
48	chr7:127360600-127372800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:127360600-127382000	Strong transcription	Hela-S3	cervix
50	chr7:127360800-127377600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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