Variant report

Variant	rs7760178
Chromosome Location	chr6:144000856-144000857
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144000686..144002814-chr6:144004185..144006059,2	K562	blood:
2	chr6:143999648..144001739-chr6:144006166..144008073,2	K562	blood:
3	chr6:143999802..144002439-chr6:144003209..144005357,2	MCF-7	breast:
4	chr6:143997590..144001098-chr6:144164062..144165676,3	K562	blood:

Variant related genes	Relation type
ENSG00000135521	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11155318	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11155320	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs11962519	0.91[CHB][hapmap];0.84[AMR][1000 genomes]
rs12530310	0.92[ASN][1000 genomes]
rs13190772	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs13191259	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13204954	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13220613	0.82[CHB][hapmap]
rs2024693	0.87[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051008	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2092762	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474150	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs3924968	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4299843	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4523103	0.87[CHB][hapmap];0.82[EUR][1000 genomes]
rs6570571	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570572	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570573	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913687	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914940	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6916245	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931556	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7450663	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7738179	1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740883	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.90[ASN][1000 genomes]
rs7741628	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7741901	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741998	0.95[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7747182	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7758298	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7762598	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764549	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7766091	0.87[CHB][hapmap]
rs7766510	0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs7770812	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7771214	1.00[CHB][hapmap]
rs7772898	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773502	1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[MEX][hapmap]
rs910419	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.91[ASN][1000 genomes]
rs9321933	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321934	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321935	0.86[JPT][hapmap]
rs9376773	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376774	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376775	0.91[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376777	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9390127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399454	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399459	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403520	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403522	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9484794	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9496718	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs9496721	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs9496729	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9496733	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[MEX][hapmap]
rs9496734	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496735	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758084	chr6:143916621-144079976	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759476	chr6:143916621-144079976	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1032369	chr6:143925374-144007513	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv604805	chr6:143930404-144005949	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7760178	STX11	cis	parietal	SCAN
rs7760178	PLAGL1	cis	lymphoblastoid	seeQTL
rs7760178	AIG1	cis	parietal	SCAN
rs7760178	FBXO30	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143997600-144001800	Active TSS	Aorta	Aorta
2	chr6:143998200-144002800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:143998400-144001600	Active TSS	Fetal Muscle Trunk	muscle
4	chr6:143998400-144001800	Active TSS	Fetal Muscle Leg	muscle
5	chr6:143998600-144001000	Active TSS	Rectal Mucosa Donor 31	rectum
6	chr6:143998600-144001200	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr6:143998600-144001400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr6:143998600-144001400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:143998600-144001400	Active TSS	Fetal Kidney	kidney
10	chr6:143998600-144001600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:143998600-144001600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr6:143998600-144001800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:143998600-144002000	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:143998600-144002000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:143998600-144002000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:143998600-144002000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:143998600-144002000	Active TSS	Right Ventricle	heart
18	chr6:143998600-144002000	Active TSS	NHDF-Ad	bronchial
19	chr6:143998600-144002200	Active TSS	Stomach Smooth Muscle	stomach
20	chr6:143998600-144002400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:143998800-144001000	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr6:143998800-144001000	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr6:143998800-144001000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:143998800-144001000	Active TSS	NHLF	lung
25	chr6:143998800-144001000	Active TSS	Osteobl	bone
26	chr6:143998800-144001200	Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:143998800-144001200	Active TSS	Fetal Lung	lung
28	chr6:143998800-144001400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:143998800-144001400	Active TSS	Fetal Stomach	stomach
30	chr6:143998800-144001400	Active TSS	HSMM	muscle
31	chr6:143998800-144001600	Active TSS	Hela-S3	cervix
32	chr6:143998800-144001800	Active TSS	Psoas Muscle	Psoas
33	chr6:143998800-144001800	Active TSS	HSMMtube	muscle
34	chr6:143998800-144002000	Active TSS	Placenta	Placenta
35	chr6:143998800-144002000	Active TSS	Ovary	ovary
36	chr6:143998800-144002200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr6:143999000-144001000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:143999000-144001000	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:143999000-144001200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:143999000-144001600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr6:143999000-144001600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:143999600-144003000	Active TSS	Right Atrium	heart
43	chr6:143999800-144003400	Weak transcription	Gastric	stomach
44	chr6:144000000-144003400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr6:144000000-144005600	Weak transcription	Small Intestine	intestine
46	chr6:144000200-144001000	Flanking Active TSS	NHEK	skin
47	chr6:144000200-144001400	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:144000200-144001600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr6:144000200-144001800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:144000200-144002200	Flanking Active TSS	Adipose Nuclei	Adipose

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