Variant report

Variant	rs9470080
Chromosome Location	chr6:35646435-35646436
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35631234..35632960-chr6:35644504..35646963,2	MCF-7	breast:
2	chr6:35634752..35642579-chr6:35643861..35648037,11	K562	blood:
3	chr6:35646147..35649006-chr6:35694213..35696052,2	K562	blood:

Variant related genes	Relation type
ENSG00000265527	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10947563	0.88[EUR][1000 genomes]
rs12153967	0.80[EUR][1000 genomes]
rs1360780	0.81[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1591365	0.86[EUR][1000 genomes]
rs2395634	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2395635	0.87[CHB][hapmap];0.81[EUR][1000 genomes]
rs3798347	0.81[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3800372	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800373	0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap]
rs4711429	0.81[CHB][hapmap]
rs4713903	0.92[EUR][1000 genomes]
rs4713904	0.90[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4713906	0.89[EUR][1000 genomes]
rs4713911	0.86[EUR][1000 genomes]
rs4713916	0.81[EUR][1000 genomes]
rs6457839	0.90[EUR][1000 genomes]
rs6899478	0.88[EUR][1000 genomes]
rs6902124	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6902321	0.81[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes]
rs6912833	0.89[EUR][1000 genomes]
rs6929523	0.88[EUR][1000 genomes]
rs6931118	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7751598	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7759392	0.87[EUR][1000 genomes]
rs7763535	0.87[EUR][1000 genomes]
rs9296158	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9296159	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9357201	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357202	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368878	0.81[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9368881	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368885	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380525	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380526	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394309	0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs9394311	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9394314	0.81[CHB][hapmap]
rs943297	0.82[CHB][hapmap];0.91[GIH][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs9462103	0.82[EUR][1000 genomes]
rs9462104	0.81[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758048	chr6:35463741-35806504	Genic enhancers Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759420	chr6:35463741-35806504	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv602924	chr6:35505311-35750299	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv885801	chr6:35537406-35671651	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	esv3430300	chr6:35549151-35959004	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv5258	chr6:35601724-35658344	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv821646	chr6:35604428-35802594	Enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv1801712	chr6:35614026-35646435	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
9	esv1809645	chr6:35619554-35646435	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
10	nsv885802	chr6:35621781-35787417	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
11	nsv885803	chr6:35621781-35805133	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
12	nsv885804	chr6:35621781-35809776	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	esv1796766	chr6:35626500-35646435	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
14	esv1797015	chr6:35626500-35646435	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
15	esv1811106	chr6:35626500-35646435	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
16	esv1848709	chr6:35626500-35655890	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	8 gene(s)	inside rSNPs	diseases
17	esv1851034	chr6:35626500-35656400	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
18	esv1840748	chr6:35629669-35656400	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	13 gene(s)	inside rSNPs	diseases
19	nsv428143	chr6:35637083-35806504	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9470080	MDGA1	cis	cerebellum	SCAN
rs9470080	FKBP5	Cis_1M	lymphoblastoid	RTeQTL
rs9470080	BRPF3	cis	cerebellum	SCAN
rs9470080	ANKS1A	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35631200-35655000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:35631400-35654400	Weak transcription	Aorta	Aorta
3	chr6:35631600-35646600	Weak transcription	Gastric	stomach
4	chr6:35631600-35652000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:35633000-35648000	Weak transcription	Right Ventricle	heart
6	chr6:35633000-35653600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:35635000-35655000	Weak transcription	Fetal Intestine Small	intestine
8	chr6:35636200-35650800	Weak transcription	Lung	lung
9	chr6:35637400-35646600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:35637600-35654400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:35637800-35653400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr6:35637800-35654400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:35637800-35655200	Weak transcription	Fetal Stomach	stomach
14	chr6:35638000-35654400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:35638200-35654400	Weak transcription	Primary B cells from cord blood	blood
16	chr6:35640400-35647200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:35640800-35646800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:35641000-35646600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:35641000-35646600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:35641400-35655000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:35641600-35646600	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr6:35641600-35647000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr6:35641600-35648400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:35641800-35646600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:35641800-35653400	Weak transcription	Esophagus	oesophagus
26	chr6:35642000-35646600	Weak transcription	Fetal Thymus	thymus
27	chr6:35642000-35651200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr6:35642800-35651800	Weak transcription	Brain Substantia Nigra	brain
29	chr6:35643200-35647000	Genic enhancers	Primary T cells from cord blood	blood
30	chr6:35643400-35646600	Weak transcription	Spleen	Spleen
31	chr6:35643800-35651000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr6:35644200-35648600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:35644400-35646800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:35644400-35646800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:35644400-35647000	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr6:35644600-35647000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:35644800-35647200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:35644800-35649800	Weak transcription	Brain Hippocampus Middle	brain
39	chr6:35644800-35653000	Weak transcription	Brain Anterior Caudate	brain
40	chr6:35644800-35653800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr6:35644800-35655200	Weak transcription	Fetal Kidney	kidney
42	chr6:35645000-35647000	Strong transcription	GM12878-XiMat	blood
43	chr6:35645000-35653800	Weak transcription	HepG2	liver
44	chr6:35645200-35646800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:35645200-35646800	Genic enhancers	Thymus	Thymus
46	chr6:35645200-35647000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:35645200-35647000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:35645200-35647000	Genic enhancers	HSMM	muscle
49	chr6:35645200-35648600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:35645400-35646600	Enhancers	NHLF	lung

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