Variant report

Variant	rs7956305
Chromosome Location	chr12:29461572-29461573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1006410	0.81[CEU][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1072724	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10743656	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771514	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771517	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843376	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10843385	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11050168	0.95[AFR][1000 genomes]
rs12301475	0.82[AFR][1000 genomes]
rs12578931	0.81[CEU][hapmap];0.82[AMR][1000 genomes]
rs12581107	0.82[AMR][1000 genomes]
rs17715086	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2016832	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288128	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2288129	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2350315	0.80[EUR][1000 genomes]
rs3782505	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3782510	0.81[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4277150	0.95[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs6487807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7298031	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299283	0.81[CEU][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7313552	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7315346	0.92[AFR][1000 genomes]
rs7358667	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7959145	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7961943	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964831	0.81[CEU][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7980218	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986072	0.84[AMR][1000 genomes];0.85[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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv975465	chr12:29456482-29462628	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1795347	chr12:29458556-29471835	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7956305	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
5	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:29439600-29464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:29439600-29469400	Weak transcription	NH-A	brain
9	chr12:29446200-29465000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:29452800-29465200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:29452800-29494200	Weak transcription	Lung	lung
13	chr12:29453000-29465200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
15	chr12:29453200-29461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:29453800-29480000	Weak transcription	Gastric	stomach
17	chr12:29454400-29463800	Weak transcription	HUVEC	blood vessel
18	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
19	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
20	chr12:29456000-29469600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:29456600-29465800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:29456600-29471000	Weak transcription	Fetal Intestine Small	intestine
23	chr12:29457000-29465200	Weak transcription	Adipose Nuclei	Adipose
24	chr12:29457000-29467400	Weak transcription	Left Ventricle	heart
25	chr12:29457600-29470600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr12:29458600-29467400	Weak transcription	Brain Anterior Caudate	brain
27	chr12:29459200-29462600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:29459200-29464800	Weak transcription	Dnd41	blood
29	chr12:29459400-29471400	Weak transcription	Liver	Liver
30	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr12:29459600-29472800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:29459600-29476000	Weak transcription	Fetal Thymus	thymus
33	chr12:29459800-29465000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:29460000-29461800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:29460200-29476000	Weak transcription	Fetal Stomach	stomach
36	chr12:29460400-29467200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr12:29460600-29461600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:29460600-29463800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr12:29460800-29470000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr12:29461200-29463600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:29461200-29486200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:29461400-29468000	Weak transcription	Primary T cells from cord blood	blood

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