Variant report

Variant	rs7760229
Chromosome Location	chr6:12336616-12336617
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:12330915..12334155-chr6:12334557..12337652,4	MCF-7	breast:
2	chr6:12334684..12338495-chr6:12601701..12604234,4	MCF-7	breast:
3	chr6:12335254..12337743-chr6:12443922..12445535,2	MCF-7	breast:
4	chr6:12334406..12337144-chr6:12347529..12350449,2	MCF-7	breast:
5	chr6:12286691..12293887-chr6:12327157..12336724,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078401	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10478736	1.00[JPT][hapmap]
rs12110345	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1626492	1.00[CHB][hapmap]
rs16872628	0.83[AMR][1000 genomes]
rs16872650	0.90[AMR][1000 genomes]
rs16872653	0.83[AMR][1000 genomes]
rs16872657	1.00[JPT][hapmap]
rs16872662	1.00[JPT][hapmap]
rs16872679	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872704	0.82[EUR][1000 genomes]
rs1794849	1.00[CHB][hapmap]
rs6903351	0.81[EUR][1000 genomes]
rs6912834	1.00[CHB][hapmap]
rs6927883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73367561	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776339	1.00[JPT][hapmap]
rs9471486	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471496	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9471517	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508394	chr6:12285464-12386745	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7760229	TBC1D7	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12327800-12337000	Enhancers	HepG2	liver
2	chr6:12331000-12337200	Enhancers	Fetal Intestine Large	intestine
3	chr6:12331000-12337200	Enhancers	Fetal Intestine Small	intestine
4	chr6:12332000-12340200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:12332200-12344000	Weak transcription	Aorta	Aorta
6	chr6:12332600-12340400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:12334400-12337000	Enhancers	Stomach Mucosa	stomach
8	chr6:12334600-12337200	Enhancers	Hela-S3	cervix
9	chr6:12334800-12337000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:12335000-12337000	Enhancers	Liver	Liver
11	chr6:12335000-12342000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:12335000-12342000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr6:12335200-12337000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:12335200-12337200	Enhancers	A549	lung
15	chr6:12335400-12337000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:12335400-12337000	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr6:12335400-12337000	Enhancers	Pancreas	Pancrea
18	chr6:12335600-12337200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr6:12335800-12336800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:12335800-12336800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:12335800-12336800	Enhancers	Small Intestine	intestine
22	chr6:12335800-12337200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr6:12336000-12336800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr6:12336000-12336800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:12336000-12336800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr6:12336000-12336800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:12336000-12336800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr6:12336000-12337000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:12336000-12337000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr6:12336000-12343400	Weak transcription	Fetal Kidney	kidney
31	chr6:12336200-12336800	Enhancers	Placenta	Placenta
32	chr6:12336200-12337000	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:12336400-12336800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr6:12336400-12336800	Enhancers	H9 Cell Line	embryonic stem cell
35	chr6:12336400-12336800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:12336400-12336800	Enhancers	Duodenum Mucosa	Duodenum
37	chr6:12336400-12337000	Flanking Active TSS	GM12878-XiMat	blood
38	chr6:12336400-12337400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:12336400-12340000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:12336600-12336800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:12336600-12336800	Enhancers	Adipose Nuclei	Adipose
42	chr6:12336600-12336800	Enhancers	Left Ventricle	heart
43	chr6:12336600-12336800	Enhancers	Lung	lung
44	chr6:12336600-12336800	Enhancers	Stomach Smooth Muscle	stomach
45	chr6:12336600-12337000	Enhancers	Rectal Mucosa Donor 29	rectum

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