Variant report

Variant	rs9379897
Chromosome Location	chr6:26601526-26601527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26600684..26602310-chr6:27048810..27050744,2	MCF-7	breast:
2	chr6:26575403..26577801-chr6:26599976..26601665,3	K562	blood:
3	chr6:26597702..26602573-chr6:27112472..27116781,7	MCF-7	breast:
4	chr6:26330749..26333675-chr6:26599169..26602051,2	K562	blood:
5	chr6:26592995..26594553-chr6:26600001..26601767,2	K562	blood:
6	chr6:26599209..26601665-chr6:27091751..27095909,4	K562	blood:
7	chr6:26599541..26602825-chr6:26986557..26990306,3	K562	blood:
8	chr6:26599531..26602687-chr6:27093072..27095909,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000224843	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000238621	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 33 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10484443	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs11967852	0.86[ASN][1000 genomes]
rs12176129	0.83[AMR][1000 genomes]
rs13195210	0.83[ASN][1000 genomes]
rs13195509	0.85[CEU][hapmap]
rs13208916	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13210025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13214027	0.92[CEU][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs13215020	0.80[ASN][1000 genomes]
rs13220261	0.81[CEU][hapmap]
rs16891725	0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap]
rs16891790	1.00[CHB][hapmap]
rs16901784	0.93[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes]
rs2093169	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs28360517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734542	0.83[CEU][hapmap]
rs3734544	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs3757150	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs3799383	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs3823158	0.85[CEU][hapmap]
rs3999471	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4634439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[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];1.00[ASN][1000 genomes]
rs67234939	0.89[AMR][1000 genomes]
rs6911765	0.86[CHB][hapmap]
rs6920256	0.93[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.88[AMR][1000 genomes]
rs6936555	0.83[ASN][1000 genomes]
rs6936561	0.83[ASN][1000 genomes]
rs7740197	1.00[JPT][hapmap]
rs7759969	0.92[JPT][hapmap]
rs7773938	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9295702	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9348718	0.86[CHB][hapmap]
rs9348726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348727	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs9348728	0.83[ASN][1000 genomes]
rs9358944	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9358945	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9358946	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9366658	0.86[CHB][hapmap];0.92[JPT][hapmap]
rs9368442	0.88[ASN][1000 genomes]
rs9368443	0.89[ASN][1000 genomes]
rs9368445	0.83[ASN][1000 genomes]
rs9368447	0.83[ASN][1000 genomes]
rs9368448	0.83[ASN][1000 genomes]
rs9368450	0.80[ASN][1000 genomes]
rs9368451	0.80[ASN][1000 genomes]
rs9379891	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9379893	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379895	0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9379899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379901	1.00[CHB][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379905	0.83[ASN][1000 genomes]
rs9379907	0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9393735	0.92[CEU][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs9393737	0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9393739	0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:33)

SNP	Gene	Cis/trans	Tissue	Source
rs9379897	BTN3A2	cis	multi-tissue	Pritchard
rs9379897	BTN3A2	cis	normal skin	skin_eQTL
rs9379897	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9379897	ZSCAN23	cis	parietal	SCAN
rs9379897	BTN3A2	cis	lymphoblastoid	seeQTL
rs9379897	ZNF323	cis	parietal	SCAN
rs9379897	BTN3A2	cis	Nerve Tibial	GTEx
rs9379897	HIST1H2BD	cis	cerebellum	SCAN
rs9379897	HIST1H3A	cis	cerebellum	SCAN
rs9379897	BTN3A2	cis	cerebellum	SCAN
rs9379897	BTN3A2	cis	Muscle Skeletal	GTEx
rs9379897	CMAH	cis	parietal	SCAN
rs9379897	BTN3A2	cis	Heart Left Ventricle	GTEx
rs9379897	LRRC16A	cis	parietal	SCAN
rs9379897	ZNF192	cis	cerebellum	SCAN
rs9379897	BTN3A2	cis	Esophagus Mucosa	GTEx
rs9379897	BTN3A2	cis	lymphoblastoid	GTEx
rs9379897	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9379897	BTN3A2	cis	Thyroid	GTEx
rs9379897	HIST1H2BC	cis	parietal	SCAN
rs9379897	BTN3A2	cis	Artery Tibial	GTEx
rs9379897	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs9379897	ZKSCAN3	cis	parietal	SCAN
rs9379897	LOC100270746	cis	lymphoblastoid	seeQTL
rs9379897	BTN3A2	cis	Whole Blood	GTEx
rs9379897	BTN3A3	cis	lymphoblastoid	seeQTL
rs9379897	BTN3A2	cis	lung	GTEx
rs9379897	HIST1H4L	cis	parietal	SCAN
rs9379897	BTN3A2	cis	uninvolved skin	skin_eQTL
rs9379897	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9379897	ZSCAN23	cis	cerebellum	SCAN
rs9379897	BTN3A2	cis	Artery Aorta	GTEx
rs9379897	BTN3A2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26598000-26604800	Weak transcription	Aorta	Aorta
2	chr6:26598000-26606800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:26598200-26607800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:26598600-26601600	Strong transcription	Fetal Thymus	thymus
5	chr6:26598600-26601800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr6:26598600-26603200	Weak transcription	Fetal Brain Male	brain
7	chr6:26598800-26602800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:26599000-26601600	Weak transcription	Psoas Muscle	Psoas
9	chr6:26599200-26602800	Weak transcription	Pancreas	Pancrea
10	chr6:26599200-26603000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:26599200-26603000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:26599200-26607800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:26599200-26607800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr6:26599200-26607800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:26599400-26601800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:26599400-26601800	Weak transcription	Right Ventricle	heart
17	chr6:26599400-26602000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:26599400-26602000	Weak transcription	Small Intestine	intestine
19	chr6:26599400-26607800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:26599600-26603200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr6:26599600-26607800	Weak transcription	Colonic Mucosa	Colon
22	chr6:26599800-26601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:26599800-26607800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr6:26600000-26602000	Weak transcription	HSMMtube	muscle
25	chr6:26600000-26602400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr6:26600000-26603800	Weak transcription	Gastric	stomach
27	chr6:26600000-26604400	Weak transcription	HUVEC	blood vessel
28	chr6:26600000-26607800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:26600000-26607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr6:26600000-26607800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:26600000-26607800	Weak transcription	Fetal Stomach	stomach
32	chr6:26600000-26607800	Weak transcription	Thymus	Thymus
33	chr6:26600000-26607800	Weak transcription	HepG2	liver
34	chr6:26600000-26607800	Weak transcription	NHLF	lung
35	chr6:26600000-26614000	Weak transcription	Spleen	Spleen
36	chr6:26600200-26602200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:26600200-26602600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr6:26600200-26603400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr6:26600200-26603600	Weak transcription	NH-A	brain
40	chr6:26600200-26603800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:26600200-26603800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:26600200-26604400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:26600200-26607200	Weak transcription	Brain Germinal Matrix	brain
44	chr6:26600200-26607600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:26600200-26607600	Weak transcription	Hela-S3	cervix
46	chr6:26600200-26607800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr6:26600200-26607800	Weak transcription	Brain Angular Gyrus	brain
48	chr6:26600200-26607800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:26600200-26607800	Weak transcription	Fetal Kidney	kidney
50	chr6:26600200-26607800	Weak transcription	Dnd41	blood

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