Variant report

Variant	rs6427626
Chromosome Location	chr1:161718949-161718950
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr1:161718893-161720620	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr1:161718920-161720671	PFSK-1	brain:	n/a	n/a
3	REST	chr1:161718750-161720601	H1-neurons	neurons:	n/a	chr1:161720166-161720179
4	SETDB1	chr1:161718751-161720567	U2OS	brain:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:161718394..161721019-chr17:57915124..57916843,2	MCF-7	breast:
2	chr1:161718595..161726705-chr1:161728119..161739561,22	MCF-7	breast:
3	chr1:161703503..161707776-chr1:161717836..161724077,7	K562	blood:
4	chr1:161718568..161724937-chr1:161732191..161738837,13	K562	blood:
5	chr1:161718380..161719915-chr8:144772917..144775501,2	MCF-7	breast:
6	chr1:161694367..161698874-chr1:161718174..161721030,6	MCF-7	breast:
7	chr1:161718558..161723568-chr1:161731521..161737462,16	K562	blood:
8	chr1:161718255..161719858-chr8:127569641..127571490,2	MCF-7	breast:
9	chr1:161718427..161720383-chr1:161735445..161737521,2	MCF-7	breast:
10	chr1:161704696..161707209-chr1:161718366..161721899,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FCGR3B-7	chr1:161718366-161719580	NONHSAT007202

No data

Variant related genes	Relation type
DUSP12	TF binding region
ENSG00000181135	Chromatin interaction
ENSG00000226889	Chromatin interaction
ENSG00000162746	Chromatin interaction
ENSG00000254286	Chromatin interaction
ENSG00000118217	Chromatin interaction
ENSG00000168672	Chromatin interaction
ENSG00000241347	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1027701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1027702	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1063178	0.82[GIH][hapmap]
rs12026445	0.88[CHB][hapmap]
rs12116756	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12121310	0.82[GIH][hapmap]
rs12121500	0.82[GIH][hapmap]
rs12121522	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12564653	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745240	0.93[GIH][hapmap];0.85[TSI][hapmap]
rs1340981	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1417580	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];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap]
rs2174208	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4656332	0.81[EUR][1000 genomes]
rs4657096	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657097	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4657098	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6427624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6427625	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7540096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6427626	DUSP12	cis	lymphoblastoid	seeQTL
rs6427626	C1orf61	cis	cerebellum	SCAN
rs6427626	ARHGEF11	cis	cerebellum	SCAN
rs6427626	PEAR1	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161707600-161719200	Weak transcription	NHLF	lung
2	chr1:161714000-161719000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:161714600-161719000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:161714600-161719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:161714800-161719000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:161717400-161719200	Flanking Active TSS	GM12878-XiMat	blood
7	chr1:161717600-161719000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:161717600-161719200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:161717600-161719200	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:161717600-161719200	Enhancers	HepG2	liver
11	chr1:161717600-161719400	Weak transcription	Lung	lung
12	chr1:161717800-161719200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr1:161718200-161719000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:161718200-161719000	Enhancers	K562	blood
15	chr1:161718400-161719000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr1:161718400-161719000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr1:161718400-161719000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:161718400-161719000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr1:161718400-161719200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:161718400-161719200	Weak transcription	Placenta	Placenta
21	chr1:161718600-161719000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:161718600-161719000	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr1:161718600-161719000	Enhancers	A549	lung
24	chr1:161718600-161719000	Enhancers	NHEK	skin
25	chr1:161718600-161719200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:161718600-161719200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:161718600-161719200	Enhancers	Brain Anterior Caudate	brain
28	chr1:161718600-161720200	Active TSS	Fetal Brain Male	brain
29	chr1:161718800-161719000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr1:161718800-161719000	Enhancers	Primary B cells from cord blood	blood
31	chr1:161718800-161719000	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:161718800-161719000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:161718800-161719000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr1:161718800-161719000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:161718800-161719000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:161718800-161719000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:161718800-161719000	Enhancers	Adipose Nuclei	Adipose
38	chr1:161718800-161719000	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:161718800-161719000	Enhancers	Brain Substantia Nigra	brain
40	chr1:161718800-161719000	Enhancers	Fetal Brain Female	brain
41	chr1:161718800-161719000	Enhancers	Small Intestine	intestine
42	chr1:161718800-161719000	Enhancers	HMEC	breast
43	chr1:161718800-161719000	Enhancers	NH-A	brain
44	chr1:161718800-161719000	Enhancers	NHDF-Ad	bronchial
45	chr1:161718800-161719000	Enhancers	Osteobl	bone
46	chr1:161718800-161719200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:161718800-161719200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:161718800-161719200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:161718800-161719200	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr1:161718800-161719200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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