Variant report

Variant	rs1430410
Chromosome Location	chr3:156525562-156525563
allele	G/T
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:156521817..156525806-chr3:156525939..156530007,4	MCF-7	breast:
2	chr3:156523470..156525861-chr3:156534229..156535791,2	MCF-7	breast:
3	chr3:156388866..156397270-chr3:156524172..156537549,71	MCF-7	breast:
4	chr3:156522791..156525819-chr3:156530782..156532939,3	MCF-7	breast:
5	chr3:156515560..156517669-chr3:156523840..156525586,2	K562	blood:
6	chr3:156424358..156426182-chr3:156523815..156525710,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-6F2.7.1-3	chr3:156522228-156525596	NONHSAT092867

No data

Variant related genes	Relation type
ENSG00000230457	Chromatin interaction
ENSG00000240875	Chromatin interaction
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10936037	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10936038	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936040	0.82[TSI][hapmap]
rs11711674	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11717133	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12492804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497539	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072896	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13086516	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13097325	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13322318	0.82[TSI][hapmap]
rs1384538	0.82[TSI][hapmap]
rs1430411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560415	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1560416	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1835372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2653817	0.83[YRI][hapmap]
rs344071	0.83[YRI][hapmap]
rs344072	0.83[YRI][hapmap]
rs344074	0.82[YRI][hapmap]
rs4680305	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680317	0.82[TSI][hapmap]
rs59717073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6776157	0.88[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6780427	0.82[TSI][hapmap]
rs7638625	0.82[TSI][hapmap]
rs7641929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818684	0.89[TSI][hapmap];0.81[AMR][1000 genomes]
rs9820830	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9837271	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842198	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844054	0.82[TSI][hapmap]
rs9858861	0.89[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871817	0.82[TSI][hapmap]
rs9874866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428745	chr3:156405054-156577840	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv877685	chr3:156444383-156611676	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv877686	chr3:156489509-156557697	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs1430410	LINC00886	cis	Esophagus Mucosa	GTEx
rs1430410	LINC00886	cis	Artery Aorta	GTEx
rs1430410	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs1430410	LINC00886	cis	Thyroid	GTEx
rs1430410	LINC00886	cis	Artery Tibial	GTEx
rs1430410	Hs.54543	cis	multi-tissue	Pritchard
rs1430410		cis	Lymphoblastoid	GTEx
rs1430410	LINC00886	cis	Nerve Tibial	GTEx
rs1430410	LINC00886	cis	Esophagus Muscularis	GTEx
rs1430410	LINC00886	cis	lung	GTEx
rs1430410	PPM1L	cis	cerebellum	SCAN
rs1430410	LINC00886	cis	Adipose Subcutaneous	GTEx
rs1430410	LINC00886	cis	Muscle Skeletal	GTEx
rs1430410	LINC00886	cis	Stomach	GTEx

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156502800-156528400	Weak transcription	Esophagus	oesophagus
2	chr3:156502800-156529000	Weak transcription	Liver	Liver
3	chr3:156511200-156529000	Weak transcription	Primary T cells from cord blood	blood
4	chr3:156511400-156530400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:156514400-156525800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:156517400-156529000	Weak transcription	A549	lung
7	chr3:156518000-156529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:156520200-156525800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:156520200-156530400	Weak transcription	Right Ventricle	heart
10	chr3:156520400-156525800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:156522200-156525800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:156522200-156526000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:156522200-156530400	Weak transcription	Gastric	stomach
14	chr3:156522400-156529000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:156523000-156526600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:156523400-156527400	Weak transcription	GM12878-XiMat	blood
17	chr3:156524000-156526600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:156524000-156527200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:156524400-156527000	Enhancers	Osteobl	bone
20	chr3:156524800-156528200	Enhancers	NHEK	skin
21	chr3:156525000-156526400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:156525000-156529000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:156525200-156525600	Weak transcription	K562	blood
24	chr3:156525200-156526000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr3:156525200-156526000	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr3:156525200-156527400	Weak transcription	Fetal Intestine Small	intestine
27	chr3:156525200-156528400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:156525400-156526400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:156525400-156526800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr3:156525400-156527600	Weak transcription	Stomach Smooth Muscle	stomach

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