Variant report

Variant	rs7954278
Chromosome Location	chr12:29459290-29459291
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	chr12:29458406..29460957-chr12:29462899..29465425,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1035604	0.84[ASN][1000 genomes]
rs10843366	0.89[ASN][1000 genomes]
rs10843367	0.89[ASN][1000 genomes]
rs10843371	0.89[ASN][1000 genomes]
rs10843377	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10843382	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10843384	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10843403	0.87[ASN][1000 genomes]
rs11050152	0.85[ASN][1000 genomes]
rs11050157	0.87[ASN][1000 genomes]
rs11050161	0.89[ASN][1000 genomes]
rs11050162	0.89[ASN][1000 genomes]
rs11050167	0.89[ASN][1000 genomes]
rs11050170	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050173	0.89[ASN][1000 genomes]
rs11050181	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11050187	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11050188	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050189	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050190	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11050191	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11050192	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11050193	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050194	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11050208	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12228468	0.81[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12231498	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12366505	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12366527	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16934135	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1989478	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1991114	0.84[ASN][1000 genomes]
rs2042511	0.89[ASN][1000 genomes]
rs2194518	0.89[ASN][1000 genomes]
rs2194519	0.89[ASN][1000 genomes]
rs3764953	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3782506	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782509	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3782511	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4331146	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57803026	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6487796	0.89[ASN][1000 genomes]
rs6487801	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6487804	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6487805	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487808	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67146951	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67517901	0.89[ASN][1000 genomes]
rs7139273	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs7294598	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7301188	0.94[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7301398	0.90[CEU][hapmap]
rs7302129	0.89[ASN][1000 genomes]
rs7308125	0.82[CEU][hapmap];0.89[ASN][1000 genomes]
rs7311912	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7312164	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7954871	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7957339	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973786	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7976961	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs962866	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs9738721	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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
rs7954278	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:34 , 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	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
6	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:29435400-29467200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:29439600-29464000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:29439600-29469400	Weak transcription	NH-A	brain
11	chr12:29443400-29460200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr12:29446200-29465000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr12:29449600-29470800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:29452800-29465200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:29452800-29494200	Weak transcription	Lung	lung
16	chr12:29453000-29465200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:29453000-29472800	Weak transcription	Fetal Intestine Large	intestine
18	chr12:29453200-29461800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr12:29453800-29480000	Weak transcription	Gastric	stomach
20	chr12:29454400-29463800	Weak transcription	HUVEC	blood vessel
21	chr12:29454600-29475800	Weak transcription	Spleen	Spleen
22	chr12:29455200-29489400	Weak transcription	Primary B cells from cord blood	blood
23	chr12:29456000-29469600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:29456600-29465800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:29456600-29471000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:29457000-29465200	Weak transcription	Adipose Nuclei	Adipose
27	chr12:29457000-29467400	Weak transcription	Left Ventricle	heart
28	chr12:29457600-29470600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:29458000-29460000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:29458400-29459800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:29458600-29467400	Weak transcription	Brain Anterior Caudate	brain
32	chr12:29459200-29460800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr12:29459200-29462600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:29459200-29464800	Weak transcription	Dnd41	blood

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