Variant report

Variant	rs1470390
Chromosome Location	chr1:212510700-212510701
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	chr1:212507727..212512410-chr1:212514335..212517605,4	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10863960	0.81[EUR][1000 genomes]
rs10863961	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10863963	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119924	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119929	0.84[ASN][1000 genomes]
rs11119930	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs11576437	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11576769	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580285	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11584189	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585215	0.87[EUR][1000 genomes]
rs11587555	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588867	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589817	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11590242	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590672	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060029	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs12062818	0.84[ASN][1000 genomes]
rs12090970	0.88[ASN][1000 genomes]
rs12095810	0.88[ASN][1000 genomes]
rs12096035	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12411213	0.88[ASN][1000 genomes]
rs12726409	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727947	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12728266	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12734895	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737825	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12743785	1.00[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12745269	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12756678	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493600	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs17721302	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2120770	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297306	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2358448	0.89[EUR][1000 genomes]
rs2358454	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2884465	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884466	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34080686	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447409	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35822123	0.84[EUR][1000 genomes]
rs4951595	0.84[ASN][1000 genomes]
rs55814152	0.87[EUR][1000 genomes]
rs56104831	0.84[ASN][1000 genomes]
rs6661987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs6667199	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6693849	0.86[EUR][1000 genomes]
rs71646158	0.84[EUR][1000 genomes]
rs72754339	0.84[ASN][1000 genomes]
rs7518399	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7531219	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs968531	0.87[EUR][1000 genomes]
rs968532	0.87[EUR][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	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1470390	RP11-15I11.3	cis	lung	GTEx
rs1470390	RP11-15I11.3	cis	Thyroid	GTEx
rs1470390	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212467400-212526000	Weak transcription	A549	lung
2	chr1:212479200-212525400	Weak transcription	Aorta	Aorta
3	chr1:212486200-212526000	Weak transcription	HUVEC	blood vessel
4	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
5	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:212498000-212526200	Weak transcription	Fetal Brain Male	brain
7	chr1:212499800-212525400	Weak transcription	Gastric	stomach
8	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
9	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
10	chr1:212501400-212525800	Weak transcription	Pancreas	Pancrea
11	chr1:212501400-212526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:212501800-212510800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:212502200-212516600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:212502200-212526000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:212502400-212528200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:212502600-212512000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:212502800-212514000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:212503000-212519200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:212504200-212525600	Weak transcription	Spleen	Spleen
26	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
27	chr1:212504600-212513800	Strong transcription	Liver	Liver
28	chr1:212504800-212525800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:212504800-212526000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:212505000-212525600	Weak transcription	Colonic Mucosa	Colon
31	chr1:212505200-212531400	Weak transcription	HMEC	breast
32	chr1:212505400-212513400	Strong transcription	Fetal Thymus	thymus
33	chr1:212505600-212510800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:212505600-212513200	Strong transcription	Dnd41	blood
35	chr1:212505800-212520200	Weak transcription	Colon Smooth Muscle	Colon
36	chr1:212505800-212533200	Weak transcription	NH-A	brain
37	chr1:212506000-212514800	Strong transcription	Adipose Nuclei	Adipose
38	chr1:212506200-212512400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr1:212506200-212518400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr1:212506600-212512400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:212507400-212525400	Weak transcription	Esophagus	oesophagus
42	chr1:212507400-212525600	Weak transcription	Brain Anterior Caudate	brain
43	chr1:212507400-212526000	Weak transcription	HSMM	muscle
44	chr1:212507600-212519200	Weak transcription	K562	blood
45	chr1:212507600-212526000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:212507800-212519200	Weak transcription	NHDF-Ad	bronchial
47	chr1:212507800-212520800	Weak transcription	Ovary	ovary
48	chr1:212507800-212526000	Weak transcription	Fetal Brain Female	brain
49	chr1:212508000-212515000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:212508000-212515000	Weak transcription	Thymus	Thymus

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