Variant report

Variant	rs6709401
Chromosome Location	chr2:187356004-187356005
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:187353036-187357373	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187352868..187356509-chr2:187367066..187369424,5	K562	blood:
2	chr2:187354897..187356653-chr2:187371312..187373329,2	K562	blood:

Variant related genes	Relation type
DPRXP1	TF binding region
ENSG00000065548	Chromatin interaction
ENSG00000268846	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10177153	1.00[CHB][hapmap]
rs10178888	0.85[EUR][1000 genomes]
rs10181681	0.80[EUR][1000 genomes]
rs10190003	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10198525	1.00[CHB][hapmap]
rs10200749	1.00[CHB][hapmap]
rs1037241	0.93[EUR][1000 genomes]
rs10497671	1.00[CHB][hapmap]
rs10497672	0.91[CEU][hapmap];0.96[GIH][hapmap];0.86[TSI][hapmap]
rs11675633	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11675656	0.85[EUR][1000 genomes]
rs11678950	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11680486	0.93[EUR][1000 genomes]
rs11690758	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11692028	0.92[EUR][1000 genomes]
rs11692347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11693797	0.93[EUR][1000 genomes]
rs11888432	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11895483	0.82[EUR][1000 genomes]
rs11898666	0.92[EUR][1000 genomes]
rs11901465	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11903027	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13392819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13393891	0.81[EUR][1000 genomes]
rs13394241	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13401304	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13428033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1448848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1448849	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1448855	1.00[CHB][hapmap]
rs16827968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16827994	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1868383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1869031	0.83[EUR][1000 genomes]
rs2044683	0.90[EUR][1000 genomes]
rs2084488	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2084490	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2197139	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2370688	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2887826	0.94[EUR][1000 genomes]
rs35642346	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55719959	0.93[EUR][1000 genomes]
rs56137171	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61226319	0.93[EUR][1000 genomes]
rs61434493	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6434167	0.89[EUR][1000 genomes]
rs6434174	1.00[CHB][hapmap]
rs6716324	0.93[EUR][1000 genomes]
rs6717525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6724161	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6728382	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6731567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs6744717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72893450	0.89[EUR][1000 genomes]
rs72895449	0.94[EUR][1000 genomes]
rs72897386	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72901315	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72901322	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7579259	0.94[EUR][1000 genomes]
rs7584137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7585889	0.92[EUR][1000 genomes]
rs7588607	0.90[EUR][1000 genomes]
rs7603088	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9917285	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6709401	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL
rs6709401	ITGAV	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187351800-187361000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:187351800-187362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:187352000-187357800	Weak transcription	Pancreas	Pancrea
4	chr2:187352200-187365400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:187352200-187365400	Weak transcription	Lung	lung
6	chr2:187352400-187358000	Weak transcription	Fetal Muscle Leg	muscle
7	chr2:187352400-187358200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:187352400-187358400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:187352400-187358400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr2:187352400-187358600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr2:187352400-187358800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr2:187352400-187358800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:187352400-187358800	Enhancers	Colon Smooth Muscle	Colon
14	chr2:187352400-187358800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:187352400-187359000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:187352400-187359400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:187352400-187360000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:187352400-187360000	Weak transcription	Placenta	Placenta
19	chr2:187352600-187357000	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:187352600-187357000	Weak transcription	Fetal Thymus	thymus
21	chr2:187352600-187357200	Enhancers	Liver	Liver
22	chr2:187352600-187358000	Enhancers	Brain Angular Gyrus	brain
23	chr2:187352600-187358600	Enhancers	Brain Anterior Caudate	brain
24	chr2:187352600-187359800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:187352600-187360200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:187352600-187360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:187352600-187360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:187352600-187362600	Weak transcription	HSMMtube	muscle
29	chr2:187353000-187357200	Enhancers	Small Intestine	intestine
30	chr2:187353200-187357800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:187353200-187360200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:187353400-187358200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:187353400-187360000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:187353400-187361800	Weak transcription	Fetal Heart	heart
35	chr2:187353600-187357600	Active TSS	GM12878-XiMat	blood
36	chr2:187353600-187357800	Weak transcription	Stomach Mucosa	stomach
37	chr2:187353600-187358000	Weak transcription	Right Atrium	heart
38	chr2:187353600-187358000	Weak transcription	Right Ventricle	heart
39	chr2:187353600-187358000	Weak transcription	HSMM	muscle
40	chr2:187353600-187359800	Weak transcription	Osteobl	bone
41	chr2:187353600-187361200	Weak transcription	Fetal Brain Male	brain
42	chr2:187353600-187362600	Weak transcription	Fetal Stomach	stomach
43	chr2:187353800-187356200	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:187353800-187357000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:187353800-187357800	Enhancers	Primary T cells from cord blood	blood
46	chr2:187353800-187358000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr2:187353800-187358800	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr2:187353800-187358800	Genic enhancers	HepG2	liver
49	chr2:187353800-187359400	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr2:187353800-187359800	Weak transcription	Rectal Mucosa Donor 31	rectum

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