Variant report

Variant	rs4342884
Chromosome Location	chr1:171684832-171684833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:171683036..171685816-chr1:171686230..171688004,2	MCF-7	breast:
2	chr1:171611915..171613655-chr1:171683755..171685490,3	MCF-7	breast:
3	chr1:171613978..171614654-chr1:171684466..171685390,3	MCF-7	breast:
4	chr1:171624257..171625200-chr1:171684733..171685343,5	MCF-7	breast:
5	chr1:171624474..171625267-chr1:171684716..171685707,4	MCF-7	breast:
6	chr1:171682877..171685651-chr1:171749605..171752042,3	K562	blood:
7	chr1:171613874..171614671-chr1:171684707..171685402,3	MCF-7	breast:
8	chr1:171624400..171625332-chr1:171684735..171685281,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000010165	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10798598	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10798599	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10798603	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913508	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10913530	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913559	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913578	0.83[GIH][hapmap]
rs10913586	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11583530	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11805692	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11806314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12045452	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096984	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12120152	0.82[ASW][hapmap];1.00[CEU][hapmap];0.80[CHD][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12139610	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843251	0.82[YRI][hapmap]
rs2073484	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2227229	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3753539	0.83[GIH][hapmap]
rs4468194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425400	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659539	0.80[EUR][1000 genomes]
rs6662836	0.95[CEU][hapmap];0.83[JPT][hapmap]
rs6665581	1.00[CEU][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6668623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6672082	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6673782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674468	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6674774	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6682452	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685742	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]
rs6688447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700606	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs763225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9659578	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap]
rs9943293	1.00[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.97[TSI][hapmap]
rs999685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4342884	VAMP4	cis	multi-tissue	Pritchard
rs4342884	VAMP4	cis	Brain Pons	GTEx

Chromatin state (count:100 , 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	chr1:171665000-171692000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:171665600-171705600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:171665600-171708800	Weak transcription	Brain Angular Gyrus	brain
5	chr1:171666000-171685000	Weak transcription	Brain Germinal Matrix	brain
6	chr1:171666000-171705400	Weak transcription	Pancreas	Pancrea
7	chr1:171666600-171686200	Weak transcription	Gastric	stomach
8	chr1:171666800-171686800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:171666800-171692000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:171666800-171692000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:171666800-171692200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:171666800-171702400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:171667000-171685000	Weak transcription	Osteobl	bone
14	chr1:171667000-171692000	Weak transcription	Fetal Brain Female	brain
15	chr1:171667000-171692200	Weak transcription	Brain Anterior Caudate	brain
16	chr1:171667600-171692000	Weak transcription	Fetal Lung	lung
17	chr1:171667800-171688400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr1:171667800-171688800	Weak transcription	Spleen	Spleen
19	chr1:171667800-171692000	Weak transcription	Fetal Thymus	thymus
20	chr1:171668000-171685800	Weak transcription	Esophagus	oesophagus
21	chr1:171668600-171692400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:171668800-171705400	Weak transcription	Right Ventricle	heart
23	chr1:171668800-171708200	Weak transcription	Small Intestine	intestine
24	chr1:171669400-171685800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:171669600-171685800	Weak transcription	NHEK	skin
26	chr1:171669600-171705400	Weak transcription	Fetal Brain Male	brain
27	chr1:171670000-171688200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:171670600-171685600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:171670600-171692000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:171671200-171685000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr1:171672800-171685800	Weak transcription	K562	blood
32	chr1:171672800-171686200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:171672800-171692000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:171673600-171686800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:171674000-171696400	Weak transcription	HSMM	muscle
36	chr1:171674200-171686000	Weak transcription	Stomach Mucosa	stomach
37	chr1:171674600-171686000	Weak transcription	HSMMtube	muscle
38	chr1:171674600-171692200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:171674800-171696800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:171674800-171697200	Weak transcription	Ovary	ovary
41	chr1:171675200-171685000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:171675200-171686200	Weak transcription	Psoas Muscle	Psoas
43	chr1:171675400-171685800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr1:171676800-171685800	Weak transcription	HMEC	breast
45	chr1:171677000-171685600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:171677000-171692000	Weak transcription	GM12878-XiMat	blood
47	chr1:171677200-171685800	Weak transcription	Duodenum Mucosa	Duodenum
48	chr1:171677200-171685800	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:171677200-171692000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:171677200-171692200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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