Variant report

Variant	rs12669185
Chromosome Location	chr7:56020397-56020398
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:56017138..56022365-chr7:56030961..56033857,7	MCF-7	breast:
2	chr7:56018384..56020889-chr7:56129856..56132224,2	K562	blood:
3	chr7:56018437..56023114-chr7:56029023..56035214,11	K562	blood:
4	chr7:56017145..56021503-chr7:56030472..56033942,8	MCF-7	breast:
5	chr7:56018165..56022272-chr7:56129856..56132253,4	K562	blood:

Variant related genes	Relation type
ENSG00000146731	Chromatin interaction
ENSG00000146729	Chromatin interaction
ENSG00000129103	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1059309	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1078650	0.91[ASN][1000 genomes]
rs10800	0.82[CHD][hapmap];0.84[MEX][hapmap]
rs1136390	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974040	0.91[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12154231	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12155441	0.84[CHD][hapmap]
rs12532776	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12668504	0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12668532	0.84[ASW][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12673255	0.84[CHD][hapmap];0.84[MEX][hapmap]
rs12674147	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12674334	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13231257	0.90[ASN][1000 genomes]
rs2006649	0.94[ASN][1000 genomes]
rs2289062	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2331095	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34795560	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs34869068	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35791463	0.86[ASN][1000 genomes]
rs4424212	0.86[CHD][hapmap]
rs55852201	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58006921	0.95[ASN][1000 genomes]
rs58981281	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs59199266	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59849749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60160896	0.90[ASN][1000 genomes]
rs60962915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593288	0.95[CEU][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs6593291	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];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947671	0.82[CHD][hapmap];0.84[MEX][hapmap]
rs6947853	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6955639	0.84[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6970842	0.84[CHD][hapmap];0.84[MEX][hapmap]
rs6975697	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73134780	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73138774	0.92[ASN][1000 genomes]
rs73138777	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7456530	0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs7778601	0.84[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7781165	0.90[ASN][1000 genomes]
rs7798243	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7804578	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv1019400	chr7:55709827-56094540	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
7	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
8	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
9	nsv888064	chr7:55831721-56104539	Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
12	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
13	nsv1034826	chr7:55962159-56092835	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
14	nsv1033225	chr7:55962159-56094540	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
15	nsv981772	chr7:56009678-56020897	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12669185	SUMF2	cis	lymphoblastoid	seeQTL
rs12669185	ZNF713	cis	parietal	SCAN
rs12669185	SUMF2	cis	cerebellum	SCAN
rs12669185	SUMF2	cis	parietal	SCAN
rs12669185	ZNF713	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56018400-56020400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:56018600-56020600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr7:56018600-56020800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr7:56019000-56020400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr7:56019000-56020400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:56019000-56020400	Active TSS	Duodenum Mucosa	Duodenum
7	chr7:56019000-56020400	Active TSS	Fetal Intestine Small	intestine
8	chr7:56019000-56020400	Active TSS	Fetal Kidney	kidney
9	chr7:56019000-56020400	Active TSS	Rectal Smooth Muscle	rectum
10	chr7:56019000-56020400	Active TSS	A549	lung
11	chr7:56019000-56020400	Active TSS	Monocytes-CD14+_RO01746	blood
12	chr7:56019000-56020600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr7:56019000-56020600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:56019000-56020800	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr7:56019000-56020800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:56019200-56020400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr7:56019200-56020400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr7:56019200-56020400	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr7:56019200-56020400	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr7:56019200-56020400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:56019200-56020400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr7:56019200-56020400	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr7:56019200-56020400	Flanking Active TSS	Primary B cells from peripheral blood	blood
24	chr7:56019200-56020400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr7:56019200-56020400	Active TSS	Brain Cingulate Gyrus	brain
26	chr7:56019200-56020400	Active TSS	Brain Hippocampus Middle	brain
27	chr7:56019200-56020400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr7:56019200-56020400	Active TSS	Fetal Lung	lung
29	chr7:56019200-56020400	Active TSS	Ovary	ovary
30	chr7:56019200-56020400	Active TSS	Right Atrium	heart
31	chr7:56019200-56020400	Active TSS	HMEC	breast
32	chr7:56019200-56020400	Active TSS	HSMM	muscle
33	chr7:56019200-56020400	Active TSS	HSMMtube	muscle
34	chr7:56019200-56020400	Active TSS	HUVEC	blood vessel
35	chr7:56019200-56020400	Active TSS	NH-A	brain
36	chr7:56019200-56020400	Active TSS	NHEK	skin
37	chr7:56019200-56020400	Active TSS	NHLF	lung
38	chr7:56019200-56020600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr7:56019200-56020600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr7:56019200-56020600	Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr7:56019200-56020600	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr7:56019200-56020600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:56019200-56020600	Active TSS	K562	blood
44	chr7:56019200-56020800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr7:56019200-56020800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr7:56019200-56020800	Active TSS	GM12878-XiMat	blood
47	chr7:56019200-56020800	Active TSS	Hela-S3	cervix
48	chr7:56019200-56020800	Active TSS	Osteobl	bone
49	chr7:56019200-56021000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr7:56019400-56020400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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