Variant report

Variant	rs6916245
Chromosome Location	chr6:144002893-144002894
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:143998230..144000986-chr6:144001245..144005130,4	K562	blood:
2	chr6:143998977..144000615-chr6:144001616..144004213,2	MCF-7	breast:
3	chr6:144002192..144005187-chr6:144008261..144010591,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11155318	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11155320	0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11962519	0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12530310	0.92[ASN][1000 genomes]
rs13190772	0.95[CHB][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13191259	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13204954	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13220613	0.82[CHB][hapmap]
rs2024693	0.92[CEU][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2051008	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2092762	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2474150	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs3924968	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4299843	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4523103	0.87[CHB][hapmap];0.85[EUR][1000 genomes]
rs6570571	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6570572	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6570573	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913687	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6914940	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6931556	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7450663	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7738179	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740883	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[TSI][hapmap];0.90[ASN][1000 genomes]
rs7741628	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7741901	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7741998	0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7747182	1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7758298	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760178	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]
rs7762598	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7764549	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7766091	0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs7770812	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7771214	1.00[CHB][hapmap]
rs7772898	1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7773502	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs7776119	0.87[AFR][1000 genomes]
rs910419	0.95[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321933	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9321934	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9321935	0.86[JPT][hapmap];0.85[MEX][hapmap]
rs9376773	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9376774	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376775	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9376777	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9390127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399454	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9399456	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399459	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9403520	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9403522	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9403523	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9484794	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9496718	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9496721	1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9496729	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9496733	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs9496734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6916245	STX11	cis	parietal	SCAN
rs6916245	AIG1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143999600-144003000	Active TSS	Right Atrium	heart
2	chr6:143999800-144003400	Weak transcription	Gastric	stomach
3	chr6:144000000-144003400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:144000000-144005600	Weak transcription	Small Intestine	intestine
5	chr6:144000400-144003400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:144000600-144003400	Weak transcription	Esophagus	oesophagus
7	chr6:144000600-144003400	Weak transcription	Fetal Intestine Large	intestine
8	chr6:144000600-144003400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:144000600-144003400	Weak transcription	Lung	lung
10	chr6:144000600-144007800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr6:144000600-144008800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr6:144000800-144003400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:144000800-144008000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr6:144001200-144003200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:144001200-144003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:144001400-144003400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:144001400-144004000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr6:144001600-144003200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:144001600-144003200	Enhancers	HepG2	liver
20	chr6:144001600-144003400	Weak transcription	Fetal Stomach	stomach
21	chr6:144001600-144003600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:144001600-144004000	Weak transcription	Fetal Kidney	kidney
23	chr6:144001800-144003000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr6:144001800-144003400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:144001800-144003400	Weak transcription	Fetal Muscle Leg	muscle
26	chr6:144001800-144003400	Weak transcription	Psoas Muscle	Psoas
27	chr6:144001800-144007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:144001800-144008000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr6:144001800-144012200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:144002000-144003000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:144002000-144003400	Weak transcription	Left Ventricle	heart
32	chr6:144002000-144003800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:144002000-144005200	Weak transcription	Right Ventricle	heart
34	chr6:144002000-144007600	Weak transcription	Ovary	ovary
35	chr6:144002000-144007800	Weak transcription	Aorta	Aorta
36	chr6:144002000-144007800	Weak transcription	NHDF-Ad	bronchial
37	chr6:144002000-144008400	Weak transcription	Placenta	Placenta
38	chr6:144002000-144013000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr6:144002200-144003000	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr6:144002200-144003200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:144002200-144007800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:144002200-144008000	Weak transcription	Stomach Smooth Muscle	stomach
43	chr6:144002400-144005800	Weak transcription	Fetal Lung	lung
44	chr6:144002400-144007800	Weak transcription	Osteobl	bone
45	chr6:144002600-144003000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr6:144002600-144003000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:144002600-144003400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:144002600-144003400	Weak transcription	HUVEC	blood vessel
49	chr6:144002600-144004000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:144002800-144003000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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