Variant report

Variant	rs1203213
Chromosome Location	chr6:75943069-75943070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:75943060..75944585-chr6:75945080..75947516,2	MCF-7	breast:
2	chr6:75942897..75944973-chr6:75945233..75947234,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs117512	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs147523	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs15616	0.87[EUR][1000 genomes]
rs16886322	0.93[ASN][1000 genomes]
rs16886323	0.93[ASN][1000 genomes]
rs16886390	0.85[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs16886391	0.85[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1831689	0.89[ASN][1000 genomes]
rs2274901	0.85[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs240367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240368	0.92[EUR][1000 genomes]
rs240369	1.00[CEU][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs240381	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240382	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240383	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240385	0.89[EUR][1000 genomes]
rs240386	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240388	0.85[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs240389	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs240390	0.85[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs240392	0.87[EUR][1000 genomes]
rs240393	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240396	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240398	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[EUR][1000 genomes]
rs240400	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs240401	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs240402	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240403	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240404	0.89[EUR][1000 genomes]
rs240405	0.85[CEU][hapmap];0.85[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs240409	0.94[EUR][1000 genomes]
rs240410	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240418	0.81[JPT][hapmap]
rs240423	0.85[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240424	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240425	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs240429	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs240430	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs240431	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240432	0.85[CEU][hapmap];0.86[GIH][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs240716	0.86[JPT][hapmap]
rs240739	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs240740	0.86[JPT][hapmap]
rs34024604	0.81[ASN][1000 genomes]
rs3756790	0.85[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs3777503	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs381141	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs397039	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs414624	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs418485	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs429746	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs448854	0.89[EUR][1000 genomes]
rs507912	1.00[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs542717	0.92[EUR][1000 genomes]
rs545588	0.86[CHD][hapmap]
rs56705798	0.93[ASN][1000 genomes]
rs57762746	0.93[ASN][1000 genomes]
rs58104879	0.93[ASN][1000 genomes]
rs58259480	0.93[ASN][1000 genomes]
rs59338586	0.93[ASN][1000 genomes]
rs59681030	0.93[ASN][1000 genomes]
rs598034	0.86[JPT][hapmap]
rs60309896	0.93[ASN][1000 genomes]
rs60808683	0.93[ASN][1000 genomes]
rs60891734	0.93[ASN][1000 genomes]
rs612266	0.86[JPT][hapmap]
rs61293108	0.91[ASN][1000 genomes]
rs638590	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs643707	0.94[EUR][1000 genomes]
rs654428	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs683943	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs6906960	0.88[ASN][1000 genomes]
rs73463837	0.91[ASN][1000 genomes]
rs73463838	0.91[ASN][1000 genomes]
rs73463840	0.91[ASN][1000 genomes]
rs73463847	0.91[ASN][1000 genomes]
rs73463851	0.91[ASN][1000 genomes]
rs73463852	0.91[ASN][1000 genomes]
rs73463855	0.91[ASN][1000 genomes]
rs73463859	0.91[ASN][1000 genomes]
rs73463862	0.91[ASN][1000 genomes]
rs73463865	0.91[ASN][1000 genomes]
rs73463868	0.91[ASN][1000 genomes]
rs73463869	0.91[ASN][1000 genomes]
rs73463875	0.91[ASN][1000 genomes]
rs73463878	0.91[ASN][1000 genomes]
rs73463879	0.91[ASN][1000 genomes]
rs73463881	0.91[ASN][1000 genomes]
rs73463884	0.91[ASN][1000 genomes]
rs73463885	0.91[ASN][1000 genomes]
rs73463887	0.91[ASN][1000 genomes]
rs73463888	0.91[ASN][1000 genomes]
rs73463889	0.89[ASN][1000 genomes]
rs73463890	0.91[ASN][1000 genomes]
rs73463895	0.91[ASN][1000 genomes]
rs73463897	0.91[ASN][1000 genomes]
rs73463898	0.91[ASN][1000 genomes]
rs73463899	0.91[ASN][1000 genomes]
rs73463900	0.91[ASN][1000 genomes]
rs73463901	0.91[ASN][1000 genomes]
rs73465805	0.93[ASN][1000 genomes]
rs73467620	0.93[ASN][1000 genomes]
rs73467622	0.93[ASN][1000 genomes]
rs73467625	0.93[ASN][1000 genomes]
rs73467626	0.93[ASN][1000 genomes]
rs73467628	0.93[ASN][1000 genomes]
rs73467636	0.93[ASN][1000 genomes]
rs73467639	0.93[ASN][1000 genomes]
rs73467641	0.93[ASN][1000 genomes]
rs73467644	0.93[ASN][1000 genomes]
rs73467651	0.93[ASN][1000 genomes]
rs73467652	0.93[ASN][1000 genomes]
rs73467656	0.93[ASN][1000 genomes]
rs73467659	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016804	chr6:75775846-76188585	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538310	chr6:75775846-76188585	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv463155	chr6:75789526-75980419	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv603762	chr6:75789526-75980419	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1024079	chr6:75848556-76238519	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1027915	chr6:75893542-76510113	Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv538311	chr6:75893542-76510113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
8	nsv603763	chr6:75923605-76009426	Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1203213	TMEM30A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75917600-75946600	Weak transcription	Lung	lung
2	chr6:75922600-75947000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:75930400-75944000	Weak transcription	Ovary	ovary
4	chr6:75933200-75945400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr6:75933200-75945600	Weak transcription	HSMM	muscle
6	chr6:75934000-75948800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:75934400-75943600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:75934400-75946400	Weak transcription	Fetal Intestine Large	intestine
9	chr6:75934600-75946800	Weak transcription	Fetal Lung	lung
10	chr6:75934600-75948600	Weak transcription	Pancreas	Pancrea
11	chr6:75935000-75947200	Weak transcription	HepG2	liver
12	chr6:75936400-75945800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr6:75936400-75946800	Weak transcription	HUVEC	blood vessel
14	chr6:75940200-75946200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:75940400-75944000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:75940400-75945800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:75940400-75946000	Weak transcription	Liver	Liver
18	chr6:75940400-75946200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:75940400-75946800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:75940400-75947600	Weak transcription	Fetal Intestine Small	intestine
21	chr6:75940400-75948000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr6:75940400-75952600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr6:75940600-75943800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:75940600-75943800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr6:75940600-75944000	Weak transcription	Brain Angular Gyrus	brain
26	chr6:75940600-75944200	Weak transcription	Osteobl	bone
27	chr6:75940600-75945600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:75940600-75946400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:75940600-75946600	Weak transcription	NHEK	skin
30	chr6:75940800-75943800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:75940800-75945200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:75940800-75946400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:75940800-75946800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr6:75941000-75944800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr6:75941000-75946400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:75941200-75945400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr6:75941200-75948600	Weak transcription	Esophagus	oesophagus
38	chr6:75941400-75946800	Weak transcription	NHDF-Ad	bronchial
39	chr6:75941600-75945200	Weak transcription	Primary T cells from cord blood	blood
40	chr6:75941600-75946600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr6:75941600-75948800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:75941800-75945600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:75941800-75945800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:75942000-75945400	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr6:75942000-75946400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:75942200-75943200	Enhancers	Psoas Muscle	Psoas
47	chr6:75942200-75945800	Enhancers	Fetal Muscle Leg	muscle
48	chr6:75942400-75945800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr6:75942400-75946800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:75942600-75943400	Enhancers	H1 Cell Line	embryonic stem cell

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