Variant report

Variant	rs6837943
Chromosome Location	chr4:159096516-159096517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:159096504..159097300-chr8:35345684..35346534,2	MCF-7	breast:
2	chr15:50645802..50647418-chr4:159095561..159097188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10021199	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs10517685	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10517686	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11100152	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11933839	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11939690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17036992	0.90[EUR][1000 genomes]
rs17036995	0.90[EUR][1000 genomes]
rs17037201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17037232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17212066	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17212714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17271385	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17279270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2881374	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4234916	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap]
rs4508943	1.00[CHB][hapmap]
rs4510503	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs6820988	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs6834839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72691615	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691620	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691622	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691627	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691629	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691631	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691632	0.90[EUR][1000 genomes]
rs72691633	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691634	0.90[EUR][1000 genomes]
rs72691636	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691649	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72695726	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72695736	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72695741	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695744	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695745	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695747	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695748	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695749	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695750	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695751	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72695753	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7678302	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9997618	0.88[CEU][hapmap];1.00[CHB][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	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6837943	RP11-597D13.9	cis	Esophagus Muscularis	GTEx
rs6837943	TMEM144	cis	Nerve Tibial	GTEx
rs6837943	RP11-597D13.9	cis	Skin Sun Exposed Lower leg	GTEx
rs6837943	TMEM144	cis	Esophagus Muscularis	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159092600-159104000	Weak transcription	Lung	lung
2	chr4:159092800-159097400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:159093800-159100000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:159094000-159097400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:159094000-159097400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:159094000-159097400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr4:159094200-159097200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:159094200-159097200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:159094200-159097200	Weak transcription	Psoas Muscle	Psoas
10	chr4:159094200-159097200	Weak transcription	NH-A	brain
11	chr4:159094200-159097200	Weak transcription	NHEK	skin
12	chr4:159094200-159097400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:159094200-159097400	Weak transcription	Pancreas	Pancrea
14	chr4:159094200-159097400	Weak transcription	Small Intestine	intestine
15	chr4:159094200-159099200	Weak transcription	Placenta	Placenta
16	chr4:159094400-159096600	Enhancers	Fetal Intestine Small	intestine
17	chr4:159094400-159097200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr4:159094400-159097200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr4:159094400-159097200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:159094400-159097200	Weak transcription	HSMM	muscle
21	chr4:159094400-159097400	Weak transcription	Gastric	stomach
22	chr4:159094400-159098400	Enhancers	HMEC	breast
23	chr4:159094400-159103200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr4:159094600-159096600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr4:159094600-159097600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:159094600-159098800	Enhancers	Adipose Nuclei	Adipose
27	chr4:159094600-159098800	Enhancers	Fetal Intestine Large	intestine
28	chr4:159094800-159097400	Weak transcription	Stomach Mucosa	stomach
29	chr4:159094800-159097400	Weak transcription	Osteobl	bone
30	chr4:159094800-159100000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:159095000-159097200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:159095000-159100400	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr4:159095000-159103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:159095200-159096600	Enhancers	Fetal Heart	heart
35	chr4:159095200-159097200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:159095200-159097400	Weak transcription	Aorta	Aorta
37	chr4:159095200-159097400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr4:159095200-159097600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr4:159095400-159096800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:159095400-159099600	Weak transcription	Brain Substantia Nigra	brain
41	chr4:159095600-159097200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:159095600-159097200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:159095600-159097200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:159095600-159097600	Weak transcription	Brain Angular Gyrus	brain
45	chr4:159095800-159113800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr4:159096000-159097400	Weak transcription	Colon Smooth Muscle	Colon
47	chr4:159096000-159097400	Enhancers	HUVEC	blood vessel
48	chr4:159096000-159097600	Weak transcription	Spleen	Spleen
49	chr4:159096200-159103200	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:159096400-159097200	Weak transcription	Ovary	ovary

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