Variant report

Variant	rs3734544
Chromosome Location	chr6:26468660-26468661
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26420998..26423545-chr6:26468256..26470657,2	K562	blood:
2	chr6:26466421..26470294-chr6:26518422..26522122,3	K562	blood:
3	chr6:26457696..26459779-chr6:26466915..26469338,2	MCF-7	breast:
4	chr6:26467959..26470668-chr6:26470770..26473697,4	MCF-7	breast:
5	chr6:26466276..26469002-chr6:26480212..26482850,2	K562	blood:
6	chr6:26464945..26466980-chr6:26467631..26469867,2	K562	blood:

Variant related genes	Relation type
ENSG00000112763	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000199289	Chromatin interaction
ENSG00000124549	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10484443	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs12173854	0.85[CEU][hapmap]
rs12174602	0.85[CEU][hapmap]
rs12174631	0.81[CEU][hapmap]
rs12176129	0.84[ASN][1000 genomes]
rs12176317	0.85[CEU][hapmap]
rs13195047	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13210025	0.86[JPT][hapmap]
rs13214027	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13216828	0.85[CEU][hapmap]
rs16891717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16891725	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.97[ASN][1000 genomes]
rs16891790	1.00[CHB][hapmap]
rs16901784	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1977	0.85[CEU][hapmap]
rs1978	0.85[CEU][hapmap]
rs1979	0.84[CEU][hapmap]
rs2072803	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs2072806	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs2073529	0.85[CEU][hapmap]
rs2073531	0.84[CEU][hapmap]
rs2076030	0.85[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap]
rs2093169	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2295593	0.84[ASN][1000 genomes]
rs2393657	0.85[ASN][1000 genomes]
rs2393665	0.85[ASN][1000 genomes]
rs2393667	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs34313099	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3799380	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs3799383	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs3999471	0.92[JPT][hapmap]
rs4518487	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4634439	0.92[JPT][hapmap]
rs56296968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6456727	0.91[EUR][1000 genomes]
rs6456728	1.00[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs67234939	0.84[ASN][1000 genomes]
rs6900118	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs6900665	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6911765	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs6920256	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap]
rs6924727	0.86[EUR][1000 genomes]
rs6926677	0.87[EUR][1000 genomes]
rs6933213	0.86[EUR][1000 genomes]
rs6941920	0.86[EUR][1000 genomes]
rs7740197	0.92[JPT][hapmap]
rs7756567	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7759969	0.84[JPT][hapmap]
rs7773938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9295702	0.92[JPT][hapmap]
rs9348709	0.84[CEU][hapmap]
rs9348712	0.85[CEU][hapmap]
rs9348716	0.85[CEU][hapmap]
rs9348718	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs9348719	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348720	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348721	0.92[ASN][1000 genomes]
rs9357007	0.85[ASN][1000 genomes]
rs9358932	0.85[CEU][hapmap]
rs9358934	0.85[CEU][hapmap]
rs9358935	0.85[CEU][hapmap]
rs9358937	0.85[CEU][hapmap]
rs9358938	0.84[CEU][hapmap];0.89[CHB][hapmap]
rs9358944	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358945	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358947	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358948	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9366653	0.85[CEU][hapmap]
rs9366656	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs9366658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9379851	0.85[CEU][hapmap]
rs9379855	0.85[CEU][hapmap]
rs9379856	0.85[CEU][hapmap]
rs9379857	0.85[CEU][hapmap]
rs9379858	0.85[CEU][hapmap]
rs9379859	0.85[CEU][hapmap]
rs9379864	0.85[CEU][hapmap]
rs9379875	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs9379877	0.86[ASN][1000 genomes]
rs9379880	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9379882	0.84[ASN][1000 genomes]
rs9379893	0.92[JPT][hapmap]
rs9379895	0.92[JPT][hapmap]
rs9379897	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9379899	0.92[JPT][hapmap]
rs9379907	0.92[JPT][hapmap]
rs9393705	0.85[CEU][hapmap]
rs9393706	0.85[CEU][hapmap]
rs9393707	0.85[CEU][hapmap]
rs9393708	0.85[CEU][hapmap]
rs9393710	0.85[CEU][hapmap]
rs9393713	0.85[CEU][hapmap]
rs9393714	0.93[CEU][hapmap]
rs9393718	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs9393721	0.89[CHB][hapmap]
rs9393725	0.80[ASN][1000 genomes]
rs9393727	0.84[ASN][1000 genomes]
rs9393735	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9393737	0.92[JPT][hapmap]
rs9467772	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
4	nsv482729	chr6:26291011-26470898	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv482836	chr6:26352883-26520964	Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1031238	chr6:26428314-26471596	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv965689	chr6:26457033-26469487	Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv1031938	chr6:26467182-26501897	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs3734544	CMAH	cis	parietal	SCAN
rs3734544	BTN3A2	cis	Artery Tibial	GTEx
rs3734544	BTN3A2	cis	Whole Blood	GTEx
rs3734544	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs3734544	LOC100270746	cis	lymphoblastoid	seeQTL
rs3734544	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs3734544	BTN3A2	cis	lymphoblastoid	GTEx
rs3734544	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs3734544	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs3734544	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs3734544	BTN3A2	cis	lymphoblastoid	seeQTL
rs3734544	BTN3A2	cis	multi-tissue	Pritchard
rs3734544	BTN3A2	cis	lung	GTEx
rs3734544	BTN3A3	cis	lymphoblastoid	seeQTL
rs3734544	HIST1H3A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26459600-26469600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:26459600-26469600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr6:26459600-26469600	Strong transcription	A549	lung
4	chr6:26459600-26469800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:26459600-26470000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:26459600-26470200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:26459600-26470400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr6:26459800-26469800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:26460000-26469600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:26460000-26469600	Strong transcription	HSMM	muscle
11	chr6:26460000-26469600	Strong transcription	NHEK	skin
12	chr6:26460000-26470400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:26460000-26471400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:26460200-26469400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:26460200-26469600	Strong transcription	Placenta	Placenta
16	chr6:26460400-26469600	Strong transcription	NHLF	lung
17	chr6:26460600-26470200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:26461400-26469600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:26461400-26469600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:26461400-26469600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:26461400-26470200	Strong transcription	Fetal Thymus	thymus
22	chr6:26461600-26469000	Strong transcription	Hela-S3	cervix
23	chr6:26461600-26469200	Strong transcription	Colonic Mucosa	Colon
24	chr6:26461600-26469600	Strong transcription	Fetal Lung	lung
25	chr6:26461600-26469600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr6:26461600-26469600	Strong transcription	HepG2	liver
27	chr6:26461600-26469800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:26461600-26469800	Strong transcription	Fetal Muscle Leg	muscle
29	chr6:26461600-26470000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr6:26461600-26470000	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:26461600-26470200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:26461600-26470200	Strong transcription	Liver	Liver
33	chr6:26461600-26470400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:26461600-26470400	Strong transcription	Left Ventricle	heart
35	chr6:26461600-26471000	Strong transcription	Thymus	Thymus
36	chr6:26461600-26471200	Strong transcription	Fetal Intestine Small	intestine
37	chr6:26461600-26471600	Strong transcription	Fetal Stomach	stomach
38	chr6:26461600-26471600	Weak transcription	Right Atrium	heart
39	chr6:26461800-26469600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr6:26461800-26469600	Strong transcription	K562	blood
41	chr6:26462000-26469600	Strong transcription	Adipose Nuclei	Adipose
42	chr6:26462000-26469600	Strong transcription	Osteobl	bone
43	chr6:26462000-26470200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:26462000-26470400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr6:26462000-26470800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:26462000-26471000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr6:26462000-26471200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr6:26462000-26471200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:26462000-26471200	Strong transcription	Fetal Intestine Large	intestine
50	chr6:26462000-26471400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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