Variant report

Variant	rs6685742
Chromosome Location	chr1:171674774-171674775
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:171673211..171675541-chr1:171709972..171711571,2	K562	blood:

Variant related genes	Relation type
ENSG00000117533	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10798598	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798599	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10798603	0.90[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913488	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10913508	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913530	0.90[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913559	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913578	0.83[GIH][hapmap]
rs10913586	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11583530	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11805692	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11806314	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12045452	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12096984	0.90[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12120152	0.90[CEU][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12139610	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073484	0.90[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227229	0.90[CEU][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3753539	0.83[GIH][hapmap]
rs4342884	0.90[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468194	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425400	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6659539	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6662836	0.85[CEU][hapmap]
rs6665581	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6668623	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6672082	0.90[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.84[JPT][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6673782	0.88[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674468	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674688	0.90[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6674774	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6682452	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6688447	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6700606	0.90[CEU][hapmap];0.94[JPT][hapmap]
rs763225	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9659578	0.90[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9943293	0.90[CEU][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs999685	0.90[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv12447	chr1:171556291-171726822	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	esv1800458	chr1:171667663-171701129	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6685742	METTL13	cis	parietal	SCAN
rs6685742	DNM3	cis	cerebellum	SCAN
rs6685742	VAMP4	Cis_1M	lymphoblastoid	RTeQTL
rs6685742	PRDX6	cis	parietal	SCAN
rs6685742	VAMP4	cis	Brain Pons	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171664400-171685800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr1:171664800-171684800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
4	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
6	chr1:171666000-171676000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:171666000-171676600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
10	chr1:171666200-171676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:171666200-171682600	Weak transcription	Lung	lung
12	chr1:171666200-171684600	Weak transcription	Fetal Stomach	stomach
13	chr1:171666200-171684800	Weak transcription	Thymus	Thymus
14	chr1:171666600-171676600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:171666600-171684800	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:171666600-171686200	Weak transcription	Gastric	stomach
17	chr1:171666800-171675600	Weak transcription	Colonic Mucosa	Colon
18	chr1:171666800-171679200	Weak transcription	NH-A	brain
19	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:171667000-171675800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:171667000-171676600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:171667000-171676800	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:171667000-171685000	Weak transcription	Osteobl	bone
28	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
29	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:171667600-171676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr1:171667600-171681200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
33	chr1:171667800-171676400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
36	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
37	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus
38	chr1:171668200-171680200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:171668400-171676600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:171668400-171677200	Strong transcription	NHDF-Ad	bronchial
41	chr1:171668600-171684800	Weak transcription	Fetal Kidney	kidney
42	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
44	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
45	chr1:171669000-171676600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:171669000-171676600	Weak transcription	Aorta	Aorta
47	chr1:171669000-171676600	Weak transcription	Left Ventricle	heart
48	chr1:171669000-171678200	Weak transcription	NHLF	lung
49	chr1:171669400-171685800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:171669600-171685800	Weak transcription	NHEK	skin

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