Variant report

Variant	rs240431
Chromosome Location	chr6:75960109-75960110
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:75958951-75961937	K562	blood:	n/a	n/a
2	POLR2A	chr6:75959591-75960154	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:75959448-75960791	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:75960077-75960573	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:75952010..75957701-chr6:75957886..75965537,16	MCF-7	breast:
2	chr6:75959944..75962259-chr6:75992382..75994540,2	K562	blood:
3	chr6:75952974..75954563-chr6:75959436..75961084,2	MCF-7	breast:

Variant related genes	Relation type
COX7A2	TF binding region
ENSG00000112695	Chromatin interaction
ENSG00000112697	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs117512	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs1203213	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs147523	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs15616	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16886322	0.88[ASN][1000 genomes]
rs16886323	0.88[ASN][1000 genomes]
rs16886390	0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs16886391	0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs1831689	0.84[ASN][1000 genomes]
rs2274901	0.85[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs240367	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs240369	0.85[CEU][hapmap]
rs240381	0.87[EUR][1000 genomes]
rs240382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240383	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs240385	0.87[EUR][1000 genomes]
rs240386	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240388	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240389	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240390	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240392	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240393	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240394	0.81[JPT][hapmap]
rs240396	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240398	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240399	0.81[JPT][hapmap]
rs240400	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240401	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240402	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240403	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240404	0.87[EUR][1000 genomes]
rs240405	0.82[EUR][1000 genomes]
rs240409	0.82[EUR][1000 genomes]
rs240410	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs240423	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs240424	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs240425	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs240429	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs240430	0.87[EUR][1000 genomes]
rs240432	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs240739	0.83[CHB][hapmap]
rs3756790	0.85[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs3777503	0.84[CHB][hapmap]
rs381141	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs397039	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs414624	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs418485	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs429746	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs448854	0.87[EUR][1000 genomes]
rs507912	0.85[CEU][hapmap]
rs56705798	0.88[ASN][1000 genomes]
rs57762746	0.88[ASN][1000 genomes]
rs58104879	0.88[ASN][1000 genomes]
rs58259480	0.88[ASN][1000 genomes]
rs59338586	0.88[ASN][1000 genomes]
rs59681030	0.88[ASN][1000 genomes]
rs60309896	0.88[ASN][1000 genomes]
rs60808683	0.88[ASN][1000 genomes]
rs60891734	0.88[ASN][1000 genomes]
rs61293108	0.86[ASN][1000 genomes]
rs638590	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs643707	0.82[EUR][1000 genomes]
rs654428	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs683943	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs6906960	0.83[ASN][1000 genomes]
rs73463837	0.86[ASN][1000 genomes]
rs73463838	0.86[ASN][1000 genomes]
rs73463840	0.86[ASN][1000 genomes]
rs73463847	0.86[ASN][1000 genomes]
rs73463851	0.86[ASN][1000 genomes]
rs73463852	0.86[ASN][1000 genomes]
rs73463855	0.86[ASN][1000 genomes]
rs73463859	0.86[ASN][1000 genomes]
rs73463862	0.86[ASN][1000 genomes]
rs73463865	0.86[ASN][1000 genomes]
rs73463868	0.86[ASN][1000 genomes]
rs73463869	0.86[ASN][1000 genomes]
rs73463875	0.86[ASN][1000 genomes]
rs73463878	0.86[ASN][1000 genomes]
rs73463879	0.86[ASN][1000 genomes]
rs73463881	0.86[ASN][1000 genomes]
rs73463884	0.86[ASN][1000 genomes]
rs73463885	0.86[ASN][1000 genomes]
rs73463887	0.86[ASN][1000 genomes]
rs73463888	0.86[ASN][1000 genomes]
rs73463889	0.84[ASN][1000 genomes]
rs73463890	0.86[ASN][1000 genomes]
rs73463895	0.86[ASN][1000 genomes]
rs73463897	0.86[ASN][1000 genomes]
rs73463898	0.86[ASN][1000 genomes]
rs73463899	0.86[ASN][1000 genomes]
rs73463900	0.86[ASN][1000 genomes]
rs73463901	0.86[ASN][1000 genomes]
rs73465805	0.88[ASN][1000 genomes]
rs73467620	0.88[ASN][1000 genomes]
rs73467622	0.88[ASN][1000 genomes]
rs73467625	0.88[ASN][1000 genomes]
rs73467626	0.88[ASN][1000 genomes]
rs73467628	0.88[ASN][1000 genomes]
rs73467636	0.88[ASN][1000 genomes]
rs73467639	0.88[ASN][1000 genomes]
rs73467641	0.88[ASN][1000 genomes]
rs73467644	0.88[ASN][1000 genomes]
rs73467651	0.88[ASN][1000 genomes]
rs73467652	0.88[ASN][1000 genomes]
rs73467656	0.88[ASN][1000 genomes]
rs73467659	0.84[ASN][1000 genomes]
rs7741596	0.85[YRI][hapmap]

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
rs240431	TMEM30A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:75953800-75978200	Weak transcription	Gastric	stomach
2	chr6:75953800-75982200	Weak transcription	Spleen	Spleen
3	chr6:75954000-75974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:75954200-75961200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:75954200-75961400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:75954200-75962800	Weak transcription	Left Ventricle	heart
7	chr6:75954200-75963400	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:75954200-75963400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:75954200-75963800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:75954200-75964800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr6:75954200-75965000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:75954200-75965200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr6:75954200-75966400	Weak transcription	Aorta	Aorta
14	chr6:75954200-75967200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr6:75954200-75969400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:75954200-75971600	Weak transcription	K562	blood
17	chr6:75954200-75973200	Weak transcription	Psoas Muscle	Psoas
18	chr6:75954200-75978000	Weak transcription	Pancreas	Pancrea
19	chr6:75954200-75978000	Weak transcription	Small Intestine	intestine
20	chr6:75954200-75978000	Weak transcription	Stomach Mucosa	stomach
21	chr6:75954200-75978200	Weak transcription	Esophagus	oesophagus
22	chr6:75954200-75978400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:75954400-75960200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:75954400-75962400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:75954400-75962800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:75954400-75962800	Weak transcription	Liver	Liver
27	chr6:75954400-75962800	Weak transcription	HUVEC	blood vessel
28	chr6:75954400-75962800	Weak transcription	NH-A	brain
29	chr6:75954400-75963000	Weak transcription	Lung	lung
30	chr6:75954400-75963200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr6:75954400-75963400	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:75954400-75963400	Weak transcription	Placenta	Placenta
33	chr6:75954400-75963400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr6:75954400-75963600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:75954400-75963800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:75954400-75965000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:75954400-75965000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:75954400-75965000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:75954400-75965000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr6:75954400-75965600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr6:75954400-75965600	Weak transcription	Ovary	ovary
42	chr6:75954400-75967400	Weak transcription	Brain Angular Gyrus	brain
43	chr6:75954400-75968000	Weak transcription	NHEK	skin
44	chr6:75954400-75968600	Weak transcription	Fetal Brain Female	brain
45	chr6:75954400-75969000	Weak transcription	Colonic Mucosa	Colon
46	chr6:75954400-75972600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:75954400-75976800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr6:75954400-75977200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:75954400-75977600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr6:75954400-75978000	Weak transcription	Right Ventricle	heart

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