Variant report

Variant	rs7749160
Chromosome Location	chr6:35397127-35397128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35226026..35228002-chr6:35394504..35397292,2	K562	blood:
2	chr6:35380537..35383478-chr6:35394277..35398227,3	K562	blood:
3	chr6:35390370..35392093-chr6:35395033..35397221,2	K562	blood:

Variant related genes	Relation type
ENSG00000065029	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1040436	0.91[CHD][hapmap]
rs1053049	0.81[CHB][hapmap];0.90[CHD][hapmap];0.83[ASN][1000 genomes]
rs1883322	0.88[CHD][hapmap]
rs2016520	0.93[CHD][hapmap];0.83[GIH][hapmap]
rs2038067	0.94[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2038068	0.88[CHD][hapmap];0.80[GIH][hapmap]
rs2076166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2076167	0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs2076168	0.80[ASN][1000 genomes]
rs2076169	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2267665	0.94[CEU][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2267666	0.88[CHD][hapmap]
rs2267667	0.88[CHD][hapmap]
rs2267668	0.89[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2267669	0.89[ASW][hapmap];0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2395622	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2894401	0.83[CHD][hapmap];0.82[LWK][hapmap]
rs3734254	0.90[CHD][hapmap];0.80[GIH][hapmap];0.83[ASN][1000 genomes]
rs4713858	0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs6457818	0.81[ASN][1000 genomes]
rs6457819	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6899536	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs760783	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7749165	0.81[AMR][1000 genomes]
rs7751481	0.88[CHD][hapmap]
rs9380506	0.82[ASN][1000 genomes]
rs9462082	0.94[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9462083	0.82[ASN][1000 genomes]
rs9462084	0.82[ASN][1000 genomes]
rs9470015	0.94[CEU][hapmap];0.83[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9470024	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9794	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
11	nsv885800	chr6:35394247-35406153	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7749160	C6orf106	cis	cerebellum	SCAN
rs7749160	USP17	trans	lymphoblastoid	seeQTL
rs7749160	RNF8	cis	cerebellum	SCAN
rs7749160	PXT1	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35383600-35402600	Weak transcription	Fetal Heart	heart
2	chr6:35392400-35397200	Genic enhancers	NHLF	lung
3	chr6:35392600-35402800	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:35393200-35397200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr6:35394600-35398200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr6:35394600-35403000	Weak transcription	Brain Germinal Matrix	brain
7	chr6:35395000-35397200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:35395000-35398400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:35395000-35399800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:35395200-35402200	Weak transcription	Left Ventricle	heart
11	chr6:35395200-35404400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:35395400-35397200	ZNF genes & repeats	Primary B cells from cord blood	blood
13	chr6:35395400-35397200	Enhancers	Liver	Liver
14	chr6:35395400-35397200	ZNF genes & repeats	Spleen	Spleen
15	chr6:35395400-35397400	ZNF genes & repeats	Fetal Intestine Large	intestine
16	chr6:35395400-35397800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:35395400-35398200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
18	chr6:35395400-35402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr6:35395600-35402800	Weak transcription	Psoas Muscle	Psoas
20	chr6:35395800-35397200	ZNF genes & repeats	Placenta	Placenta
21	chr6:35395800-35403000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:35395800-35403200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:35396000-35397200	ZNF genes & repeats	Fetal Intestine Small	intestine
24	chr6:35396000-35397200	ZNF genes & repeats	Fetal Muscle Leg	muscle
25	chr6:35396000-35397200	Flanking Active TSS	HepG2	liver
26	chr6:35396000-35397200	ZNF genes & repeats	NHEK	skin
27	chr6:35396000-35397600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:35396000-35397600	ZNF genes & repeats	Colonic Mucosa	Colon
29	chr6:35396200-35397200	ZNF genes & repeats	Primary T cells from cord blood	blood
30	chr6:35396200-35397200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:35396200-35397200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:35396200-35397200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
33	chr6:35396200-35398000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:35396400-35397200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:35396400-35397200	Enhancers	NH-A	brain
36	chr6:35396400-35397400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:35396400-35397400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr6:35396400-35397600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr6:35396400-35402200	Weak transcription	Right Ventricle	heart
40	chr6:35396600-35397200	ZNF genes & repeats	HSMMtube	muscle
41	chr6:35396600-35397400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:35396600-35397400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:35396600-35397400	ZNF genes & repeats	NHDF-Ad	bronchial
44	chr6:35396600-35397600	ZNF genes & repeats	HSMM	muscle
45	chr6:35396600-35398400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:35396800-35397200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:35396800-35398200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
48	chr6:35397000-35397200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:35397000-35397400	ZNF genes & repeats	Osteobl	bone
50	chr6:35397000-35397600	ZNF genes & repeats	Brain Hippocampus Middle	brain

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