Variant report

Variant	rs10913578
Chromosome Location	chr1:171713468-171713469
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:171710166-171713538	K562	blood:	n/a	n/a
2	POLR2A	chr1:171710964-171713692	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr1:171710341..171715416-chr1:171748571..171752440,7	MCF-7	breast:
2	chr1:171709343..171715185-chr1:171748592..171756289,15	K562	blood:
3	chr1:171710254..171714548-chr1:171728803..171733052,4	K562	blood:
4	chr1:171709981..171712025-chr1:171713091..171714877,2	K562	blood:
5	chr1:171712949..171715185-chr1:171753608..171756289,2	K562	blood:
6	chr1:171710699..171713555-chr1:171719677..171724483,6	MCF-7	breast:
7	chr1:171710037..171714996-chr1:171734843..171738629,6	MCF-7	breast:
8	chr1:171709564..171713750-chr1:171736602..171743117,7	K562	blood:

No data

Variant related genes	Relation type
VAMP4	TF binding region
ENSG00000010165	Chromatin interaction
ENSG00000236741	Chromatin interaction
ENSG00000117533	Chromatin interaction
ENSG00000253060	Chromatin interaction
ENSG00000232261	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001373	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs10489249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10489251	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10753181	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798603	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs10913507	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10913529	0.89[GIH][hapmap];0.83[JPT][hapmap]
rs10913530	0.83[GIH][hapmap];0.82[YRI][hapmap]
rs10913565	0.83[JPT][hapmap]
rs10913582	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10913587	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11576221	0.85[GIH][hapmap]
rs11577073	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577197	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11577745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578699	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11578723	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11580522	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11583920	0.83[JPT][hapmap]
rs11590680	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590714	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12096984	0.86[YRI][hapmap]
rs12119232	0.94[ASN][1000 genomes]
rs12120152	0.89[YRI][hapmap]
rs12126566	0.90[ASN][1000 genomes]
rs15655	0.89[GIH][hapmap]
rs16843230	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16843251	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17649050	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17649068	0.99[ASN][1000 genomes]
rs17649250	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2073484	0.83[GIH][hapmap];0.89[YRI][hapmap]
rs2227229	0.86[YRI][hapmap]
rs2298914	0.83[JPT][hapmap]
rs2421911	0.90[ASN][1000 genomes]
rs3753539	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs4342884	0.83[GIH][hapmap]
rs4468194	0.82[YRI][hapmap]
rs6665581	0.89[YRI][hapmap]
rs6667559	0.85[GIH][hapmap]
rs6670427	0.83[CEU][hapmap]
rs6672082	0.85[YRI][hapmap]
rs6673782	0.89[YRI][hapmap]
rs6674688	0.83[GIH][hapmap];0.86[YRI][hapmap]
rs6685742	0.83[GIH][hapmap]
rs6700606	0.82[YRI][hapmap]
rs999685	0.82[YRI][hapmap]

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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10913578	VAMP4	cis	lymphoblastoid	seeQTL
rs10913578	VAMP4	cis	Brain Pons	GTEx
rs10913578	DCAF6	cis	cerebellum	SCAN
rs10913578	METTL13	cis	parietal	SCAN
rs10913578	VAMP4	cis	Frontal Cortex	GTEx
rs10913578	VAMP4	cis	multi-tissue	Pritchard
rs10913578	DNM3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171712000-171723400	Weak transcription	Lung	lung
2	chr1:171712200-171715800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:171712400-171713600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:171712400-171714200	Enhancers	Fetal Muscle Leg	muscle
5	chr1:171712400-171714600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:171712600-171713600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:171712600-171713600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:171712600-171713600	Enhancers	Primary T cells from cord blood	blood
9	chr1:171712600-171713800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:171712600-171713800	Enhancers	Osteobl	bone
11	chr1:171712800-171713600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr1:171712800-171713600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:171712800-171713600	Enhancers	HSMM	muscle
14	chr1:171712800-171713600	Enhancers	HSMMtube	muscle
15	chr1:171712800-171714000	Weak transcription	Aorta	Aorta
16	chr1:171712800-171714000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr1:171713000-171713600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:171713000-171713600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:171713000-171713600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:171713000-171713600	Enhancers	Brain Angular Gyrus	brain
21	chr1:171713000-171713600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr1:171713000-171713600	Enhancers	Psoas Muscle	Psoas
23	chr1:171713000-171713600	Enhancers	Hela-S3	cervix
24	chr1:171713000-171713600	Enhancers	HMEC	breast
25	chr1:171713000-171713600	Enhancers	K562	blood
26	chr1:171713000-171713600	Enhancers	NHEK	skin
27	chr1:171713000-171713600	Enhancers	NHLF	lung
28	chr1:171713000-171713800	Enhancers	Fetal Heart	heart
29	chr1:171713000-171713800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr1:171713000-171713800	Enhancers	NHDF-Ad	bronchial
31	chr1:171713000-171714400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr1:171713200-171713800	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr1:171713200-171714400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:171713400-171713600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr1:171713400-171716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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