Variant report

Variant	rs895673
Chromosome Location	chr6:25086968-25086969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25085087..25087243-chr6:25089273..25091853,2	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10214692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197057	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198209	0.82[JPT][hapmap]
rs1972205	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs303019	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3792975	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792984	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3812106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818269	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818271	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6935318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9295645	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9379716	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393612	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9467389	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv470806	chr6:25082262-25156197	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv462662	chr6:25084718-25165486	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv601166	chr6:25084718-25165486	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs895673	HIST1H2AK	cis	parietal	SCAN
rs895673	BTN3A1	cis	cerebellum	SCAN
rs895673	CMAH	cis	lymphoblastoid	seeQTL
rs895673	BTN2A1	cis	cerebellum	SCAN
rs895673	GPLD1	cis	parietal	SCAN
rs895673	CMAH	cis	parietal	SCAN
rs895673	CMAH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25079400-25093000	Weak transcription	Ovary	ovary
2	chr6:25080400-25098000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:25081200-25092000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:25081600-25088800	Weak transcription	Osteobl	bone
5	chr6:25082200-25094800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:25082600-25105200	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:25083800-25089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:25083800-25093200	Weak transcription	Colonic Mucosa	Colon
9	chr6:25084000-25087600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:25084200-25087000	Enhancers	Liver	Liver
11	chr6:25084200-25089800	Weak transcription	Hela-S3	cervix
12	chr6:25084800-25088400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr6:25084800-25099000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:25084800-25113800	Weak transcription	Gastric	stomach
15	chr6:25085000-25087000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:25085000-25088600	Weak transcription	Lung	lung
17	chr6:25085000-25088600	Enhancers	HUVEC	blood vessel
18	chr6:25085200-25087600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr6:25085200-25087600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr6:25085200-25088000	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr6:25085200-25089400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr6:25085200-25108000	Weak transcription	Colon Smooth Muscle	Colon
23	chr6:25085400-25087200	Enhancers	Primary hematopoietic stem cells	blood
24	chr6:25085400-25088200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr6:25085400-25091600	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:25085600-25087400	Enhancers	Primary B cells from cord blood	blood
27	chr6:25085600-25087800	Enhancers	Primary B cells from peripheral blood	blood
28	chr6:25085600-25088000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr6:25085800-25087000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr6:25085800-25087400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr6:25085800-25088400	Genic enhancers	Dnd41	blood
32	chr6:25086000-25087000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr6:25086000-25087000	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr6:25086000-25087000	Enhancers	GM12878-XiMat	blood
35	chr6:25086000-25087200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:25086000-25087200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr6:25086200-25087200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr6:25086200-25087200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:25086200-25087800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr6:25086200-25088600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:25086200-25096400	Strong transcription	Thymus	Thymus
42	chr6:25086400-25087400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr6:25086400-25089800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr6:25086400-25099600	Strong transcription	Placenta	Placenta
45	chr6:25086600-25087000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
46	chr6:25086600-25087000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:25086600-25087000	Genic enhancers	Adipose Nuclei	Adipose
48	chr6:25086600-25087400	Genic enhancers	Fetal Thymus	thymus
49	chr6:25086600-25087400	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr6:25086600-25087400	Genic enhancers	Monocytes-CD14+_RO01746	blood

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