Variant report

Variant	rs2394000
Chromosome Location	chr6:27686991-27686992
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27686786..27690624-chr6:27717358..27721129,5	K562	blood:
2	chr6:27683083..27685640-chr6:27686917..27688772,2	MCF-7	breast:
3	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
4	chr6:27684698..27689044-chr6:27689656..27693289,4	K562	blood:

Extended variants
information (count: 82 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10214440	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10484401	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139226	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13211701	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13215072	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985099	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200468	0.81[ASN][1000 genomes]
rs200502	0.82[CEU][hapmap]
rs2056925	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2092075	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2179094	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2179095	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2394002	0.88[EUR][1000 genomes]
rs2893929	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2893930	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2893931	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34752872	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35069907	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35957409	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4140646	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4711163	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4713118	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4713121	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6901520	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902689	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6914924	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922574	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930992	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs742046	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs742047	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs760587	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7756968	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7759217	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7760523	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772027	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773070	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776351	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9283880	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283881	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283882	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9283883	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9295742	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9295743	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9295746	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9348775	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357045	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9366700	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9366702	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368528	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368529	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368530	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9380010	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380011	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9380012	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393848	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461401	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9461405	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9461406	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9468195	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9468199	0.92[ASN][1000 genomes]
rs9468200	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468201	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468203	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468204	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468206	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9468214	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9468217	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9468219	0.89[EUR][1000 genomes]
rs9468220	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9468223	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9468229	0.89[EUR][1000 genomes];0.81[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	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	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	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
8	esv3327708	chr6:27683503-27692934	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2394000	AL022393.7	cis	Muscle Skeletal	GTEx
rs2394000	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs2394000	OR2B8P	cis	Thyroid	GTEx
rs2394000	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27662800-27688400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:27662800-27688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:27662800-27689000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:27663000-27688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:27663200-27688400	Weak transcription	HMEC	breast
6	chr6:27663400-27687800	Weak transcription	NHEK	skin
7	chr6:27671400-27687200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:27671600-27688600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:27673600-27687600	Weak transcription	Fetal Intestine Small	intestine
10	chr6:27674600-27687000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:27678800-27689000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:27679400-27688400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:27681200-27687000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:27681200-27687200	Weak transcription	HepG2	liver
15	chr6:27681200-27688200	Weak transcription	A549	lung
16	chr6:27681200-27688600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:27681200-27688600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr6:27681200-27688600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:27681200-27688800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:27681200-27688800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:27681600-27692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:27681800-27687800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:27681800-27688600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:27682000-27688600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:27682200-27687200	Weak transcription	Fetal Intestine Large	intestine
26	chr6:27682400-27688400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:27682400-27688600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:27682600-27687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:27682800-27687000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:27682800-27688600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:27686600-27687400	Enhancers	K562	blood
32	chr6:27686800-27687000	Enhancers	GM12878-XiMat	blood
33	chr6:27686800-27687400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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