Variant report

Variant	rs9468213
Chromosome Location	chr6:27706180-27706181
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1022486	0.83[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs10946938	0.91[JPT][hapmap]
rs10946940	0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.80[LWK][hapmap];0.94[MKK][hapmap]
rs200480	0.81[JPT][hapmap]
rs200951	0.94[LWK][hapmap];0.86[MEX][hapmap]
rs200988	0.91[LWK][hapmap];0.86[MEX][hapmap];0.80[YRI][hapmap]
rs200997	0.82[CHB][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.80[YRI][hapmap]
rs2056924	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2179095	0.80[TSI][hapmap]
rs2179096	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294480	0.91[JPT][hapmap]
rs2294481	0.91[JPT][hapmap]
rs4713112	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4713120	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs510987	0.89[LWK][hapmap]
rs57252182	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456799	0.88[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.84[MKK][hapmap]
rs6915266	0.88[CEU][hapmap];0.83[CHB][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap];0.92[MKK][hapmap]
rs6915987	0.86[JPT][hapmap]
rs6916878	0.83[JPT][hapmap]
rs6921256	0.93[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap]
rs6934437	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6934794	0.85[JPT][hapmap]
rs742046	0.83[TSI][hapmap]
rs7759217	0.83[TSI][hapmap]
rs7764081	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9295747	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348772	0.92[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs9366697	0.81[EUR][1000 genomes]
rs9366699	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9368527	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9380007	0.83[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9393830	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9393831	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9461405	0.86[TSI][hapmap]
rs9468209	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
4	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv970372	chr6:27695204-27708579	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv981370	chr6:27696520-27708579	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9468213	ZSCAN16	cis	parietal	SCAN
rs9468213	BTN3A3	cis	parietal	SCAN
rs9468213	HIST1H3C	cis	cerebellum	SCAN
rs9468213	BTN3A3	cis	cerebellum	SCAN
rs9468213	BTN2A1	cis	parietal	SCAN
rs9468213	AL022393.7	cis	Muscle Skeletal	GTEx
rs9468213	ZKSCAN3	cis	parietal	SCAN
rs9468213	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9468213	ZKSCAN3	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27705400-27707400	Active TSS	A549	lung
2	chr6:27705600-27706600	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:27705600-27707000	Active TSS	Duodenum Mucosa	Duodenum
4	chr6:27705600-27707000	Active TSS	GM12878-XiMat	blood
5	chr6:27705600-27710400	Weak transcription	K562	blood
6	chr6:27705800-27706200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr6:27705800-27706200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:27705800-27706200	Bivalent/Poised TSS	Fetal Heart	heart
9	chr6:27705800-27706400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr6:27705800-27706400	Enhancers	HepG2	liver
11	chr6:27705800-27706600	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:27705800-27706600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:27705800-27706600	Active TSS	Liver	Liver
14	chr6:27705800-27706600	Active TSS	Colon Smooth Muscle	Colon
15	chr6:27705800-27706600	Active TSS	HMEC	breast
16	chr6:27705800-27706600	Active TSS	NHDF-Ad	bronchial
17	chr6:27705800-27706800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:27705800-27706800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:27705800-27706800	Active TSS	Primary B cells from cord blood	blood
20	chr6:27705800-27706800	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr6:27705800-27706800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:27705800-27706800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:27705800-27706800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:27705800-27706800	Active TSS	Fetal Intestine Large	intestine
25	chr6:27705800-27706800	Active TSS	Psoas Muscle	Psoas
26	chr6:27705800-27706800	Active TSS	Right Atrium	heart
27	chr6:27705800-27706800	Bivalent/Poised TSS	Thymus	Thymus
28	chr6:27705800-27706800	Active TSS	HUVEC	blood vessel
29	chr6:27705800-27706800	Active TSS	Osteobl	bone
30	chr6:27705800-27707000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr6:27705800-27707000	Active TSS	Monocytes-CD14+_RO01746	blood
32	chr6:27705800-27707200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:27706000-27706200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
34	chr6:27706000-27706200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
35	chr6:27706000-27706200	Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr6:27706000-27706200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr6:27706000-27706200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:27706000-27706200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr6:27706000-27706200	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr6:27706000-27706400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr6:27706000-27706400	Flanking Active TSS	Primary B cells from peripheral blood	blood
42	chr6:27706000-27706400	Flanking Active TSS	Left Ventricle	heart
43	chr6:27706000-27706400	Active TSS	Lung	lung
44	chr6:27706000-27706400	Active TSS	HSMM	muscle
45	chr6:27706000-27706600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:27706000-27706600	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:27706000-27706600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:27706000-27706600	Active TSS	Primary T cells from cord blood	blood
49	chr6:27706000-27706600	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr6:27706000-27706600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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