Variant report

Variant	rs556256
Chromosome Location	chr15:59094764-59094765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11071397	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs12437928	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12438114	0.92[EUR][1000 genomes]
rs12439632	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12591310	0.90[JPT][hapmap]
rs12594276	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12900320	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12901817	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905507	0.85[CEU][hapmap]
rs12914164	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12915713	0.81[ASN][1000 genomes]
rs1551445	0.90[JPT][hapmap]
rs1678977	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2013098	0.81[ASN][1000 genomes]
rs2620360	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394222	0.82[ASN][1000 genomes]
rs28412567	0.82[ASN][1000 genomes]
rs28533385	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28537903	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28549775	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28812884	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28876251	0.81[ASN][1000 genomes]
rs34362744	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs347112	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34880782	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774311	0.81[AMR][1000 genomes]
rs4775095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs500057	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs501165	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs510759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561903	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs574683	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs596094	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs597112	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs601795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs625312	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs652193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs654857	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654870	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664936	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs684505	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs688343	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164844	0.81[AMR][1000 genomes]
rs7169205	0.90[JPT][hapmap]
rs7170538	0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs7171198	0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs7178970	0.81[AMR][1000 genomes]
rs8029301	0.90[JPT][hapmap]
rs8032298	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9744045	0.81[AMR][1000 genomes]
rs9788674	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][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	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic 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	87 gene(s)	inside rSNPs	diseases
2	esv1843037	chr15:59005922-59115159	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	esv1826703	chr15:59005922-59213678	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer 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	44 gene(s)	inside rSNPs	diseases
4	esv1798487	chr15:59027139-59213678	Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv428638	chr15:59032300-59126567	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59064600-59102800	Weak transcription	Lung	lung
2	chr15:59064600-59102800	Weak transcription	Pancreas	Pancrea
3	chr15:59064600-59103200	Weak transcription	Esophagus	oesophagus
4	chr15:59064600-59145600	Weak transcription	Gastric	stomach
5	chr15:59064800-59095400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr15:59065200-59117800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:59065800-59095000	Weak transcription	Fetal Thymus	thymus
8	chr15:59065800-59102800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr15:59065800-59103200	Weak transcription	NH-A	brain
10	chr15:59065800-59142800	Weak transcription	Aorta	Aorta
11	chr15:59066000-59095000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:59066000-59102400	Weak transcription	HSMM	muscle
13	chr15:59066200-59095000	Weak transcription	Osteobl	bone
14	chr15:59066200-59095600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:59066400-59095000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:59066400-59095000	Weak transcription	Fetal Intestine Large	intestine
17	chr15:59066600-59102400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:59067000-59094800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:59067000-59102400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:59067000-59102800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr15:59067000-59102800	Weak transcription	NHDF-Ad	bronchial
22	chr15:59067000-59157800	Weak transcription	Hela-S3	cervix
23	chr15:59067200-59094800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:59067200-59095000	Weak transcription	Fetal Lung	lung
25	chr15:59067200-59103200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:59067400-59102600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:59067400-59102800	Weak transcription	Brain Angular Gyrus	brain
28	chr15:59067400-59111400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr15:59067800-59094800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:59067800-59105000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr15:59068600-59094800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr15:59069400-59103600	Weak transcription	Brain Germinal Matrix	brain
33	chr15:59069600-59106000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:59069600-59119000	Weak transcription	Fetal Brain Male	brain
35	chr15:59069800-59095400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:59069800-59102600	Weak transcription	HUVEC	blood vessel
37	chr15:59069800-59121400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr15:59071800-59094800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr15:59072000-59105600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:59075000-59102800	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:59075000-59139800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:59075800-59102800	Weak transcription	Brain Anterior Caudate	brain
43	chr15:59077400-59102000	Weak transcription	NHLF	lung
44	chr15:59077600-59102200	Weak transcription	Fetal Brain Female	brain
45	chr15:59077800-59103000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:59077800-59122000	Weak transcription	Brain Substantia Nigra	brain
47	chr15:59077800-59153600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr15:59078200-59102800	Weak transcription	Ovary	ovary
49	chr15:59079000-59102600	Weak transcription	HSMMtube	muscle
50	chr15:59079600-59095000	Weak transcription	A549	lung

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