Variant report

Variant	rs6440967
Chromosome Location	chr3:99722396-99722397
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:99705385..99708827-chr3:99720207..99724283,4	MCF-7	breast:
2	chr3:99565835..99567427-chr3:99720922..99723380,2	MCF-7	breast:
3	chr3:99535115..99538387-chr3:99721301..99723851,3	MCF-7	breast:
4	chr3:99721792..99723539-chr3:99765840..99767973,2	MCF-7	breast:
5	chr3:99589389..99592521-chr3:99720573..99723632,4	MCF-7	breast:
6	chr3:99592735..99594887-chr3:99722394..99724729,2	MCF-7	breast:
7	chr3:99618971..99621795-chr3:99720299..99722726,2	MCF-7	breast:
8	chr3:99720503..99722744-chr3:99759089..99760779,2	MCF-7	breast:
9	chr3:99652546..99654648-chr3:99721251..99724198,2	MCF-7	breast:
10	chr3:99593399..99595369-chr3:99721874..99725950,4	MCF-7	breast:
11	chr3:99720592..99723772-chr3:99724475..99727275,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184220	Chromatin interaction
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs12488245	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1384062	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs1387647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1718235	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs2130369	0.88[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs35422475	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4577503	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4928150	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4928230	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928235	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs6798114	0.84[CEU][hapmap]
rs6802817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6808765	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7619512	0.85[ASN][1000 genomes]
rs7629487	0.92[CEU][hapmap]
rs7636776	0.83[EUR][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs766778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793440	0.82[TSI][hapmap]
rs793443	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs793446	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs793464	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs793502	0.83[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793503	0.82[TSI][hapmap]
rs796976	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs902159	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289981	0.87[CEU][hapmap]
rs9811920	0.92[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.80[EUR][1000 genomes]
rs9814549	0.84[CEU][hapmap];0.80[GIH][hapmap]
rs9837131	0.92[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv999332	chr3:99690207-99774720	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6440967	CASK	trans	lymphoblastoid	seeQTL
rs6440967	SENP7	cis	parietal	SCAN
rs6440967	EPHX1	trans	cerebellum	SCAN
rs6440967	OR5H6	cis	cerebellum	SCAN
rs6440967	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99708400-99724600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99714600-99724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:99714800-99724600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:99715800-99724200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
7	chr3:99718200-99723000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:99719200-99723200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:99719800-99723000	Enhancers	HMEC	breast
10	chr3:99720200-99727600	Enhancers	Stomach Mucosa	stomach
11	chr3:99720400-99722600	Enhancers	Duodenum Mucosa	Duodenum
12	chr3:99720400-99723000	Enhancers	Hela-S3	cervix
13	chr3:99720600-99722400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:99720600-99724400	Enhancers	Fetal Intestine Large	intestine
15	chr3:99720800-99722400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:99720800-99722400	Enhancers	Left Ventricle	heart
17	chr3:99720800-99722600	Enhancers	NH-A	brain
18	chr3:99720800-99724800	Weak transcription	Psoas Muscle	Psoas
19	chr3:99720800-99725000	Enhancers	Fetal Intestine Small	intestine
20	chr3:99721000-99722600	Enhancers	NHLF	lung
21	chr3:99721200-99722400	Enhancers	Muscle Satellite Cultured Cells	--
22	chr3:99721200-99722600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:99721200-99722600	Enhancers	Fetal Kidney	kidney
24	chr3:99721200-99722600	Enhancers	NHDF-Ad	bronchial
25	chr3:99721200-99723000	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr3:99721200-99723200	Enhancers	HepG2	liver
27	chr3:99721400-99722600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:99721400-99722600	Enhancers	Fetal Heart	heart
29	chr3:99721400-99722600	Enhancers	Osteobl	bone
30	chr3:99721400-99725000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr3:99721400-99729400	Enhancers	HUVEC	blood vessel
32	chr3:99721600-99722400	Enhancers	Right Ventricle	heart
33	chr3:99721600-99722400	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:99721600-99722400	Enhancers	Small Intestine	intestine
35	chr3:99721600-99722400	Flanking Active TSS	A549	lung
36	chr3:99721600-99722400	Enhancers	HSMM	muscle
37	chr3:99721600-99723600	Enhancers	Pancreatic Islets	Pancreatic Islet
38	chr3:99721600-99724200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:99721800-99722400	Enhancers	Aorta	Aorta
40	chr3:99721800-99724400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:99722000-99722400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:99722000-99722800	Weak transcription	Esophagus	oesophagus
43	chr3:99722000-99723400	Weak transcription	HSMMtube	muscle
44	chr3:99722000-99724200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:99722000-99724400	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:99722000-99724600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:99722000-99724600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:99722000-99724600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:99722000-99724600	Weak transcription	Gastric	stomach
50	chr3:99722000-99724600	Weak transcription	Pancreas	Pancrea

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