Variant report

Variant	rs6440991
Chromosome Location	chr3:99758465-99758466
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99756496..99759063-chr3:99760481..99762156,3	MCF-7	breast:
2	chr3:99590595..99595669-chr3:99758441..99761467,5	MCF-7	breast:
3	chr3:99757965..99760484-chr3:99766104..99767644,2	MCF-7	breast:
4	chr3:99753937..99756360-chr3:99757732..99759441,2	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12486901	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12487143	0.86[CEU][hapmap]
rs12489030	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs12494994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496041	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1387649	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1565341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3921767	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs4928233	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4928240	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414382	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6777622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6778589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792339	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs6800456	0.88[JPT][hapmap]
rs73859922	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7431827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7632345	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs7634628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641782	0.93[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs7652706	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs9824430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9827744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6440991	IFI27	trans	lymphoblastoid	seeQTL
rs6440991	ZPLD1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99716400-99758800	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99728400-99760400	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:99741200-99766800	Weak transcription	Right Ventricle	heart
5	chr3:99742400-99766400	Weak transcription	Aorta	Aorta
6	chr3:99743800-99759200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:99744200-99759400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:99746000-99758800	Weak transcription	Left Ventricle	heart
9	chr3:99746600-99762200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:99749000-99759400	Weak transcription	Stomach Mucosa	stomach
11	chr3:99751000-99759200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:99751400-99761000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:99752200-99759400	Weak transcription	Small Intestine	intestine
14	chr3:99752200-99774600	Weak transcription	Gastric	stomach
15	chr3:99752400-99759000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:99753200-99758800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:99753200-99759600	Weak transcription	Ovary	ovary
18	chr3:99753200-99761600	Weak transcription	Psoas Muscle	Psoas
19	chr3:99753400-99758800	Weak transcription	Fetal Stomach	stomach
20	chr3:99753400-99758800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:99753400-99758800	Weak transcription	NHDF-Ad	bronchial
22	chr3:99753600-99758800	Weak transcription	Osteobl	bone
23	chr3:99753600-99759000	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:99753600-99759000	Weak transcription	Fetal Kidney	kidney
25	chr3:99753600-99759000	Weak transcription	HMEC	breast
26	chr3:99753600-99759200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:99753800-99758800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:99753800-99759200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:99753800-99759200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:99754000-99759200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:99754400-99759600	Weak transcription	Fetal Intestine Small	intestine
32	chr3:99756000-99761400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:99757600-99758800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:99757600-99762400	Enhancers	Fetal Intestine Large	intestine
35	chr3:99757800-99766800	Weak transcription	Pancreas	Pancrea
36	chr3:99758200-99758600	Weak transcription	HSMM	muscle
37	chr3:99758200-99759600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:99758400-99759400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:99758400-99759400	Weak transcription	HSMMtube	muscle
40	chr3:99758400-99760600	Enhancers	HUVEC	blood vessel
41	chr3:99758400-99760800	Enhancers	Fetal Lung	lung
42	chr3:99758400-99762600	Enhancers	NHLF	lung

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