Variant report

Variant	rs9358946
Chromosome Location	chr6:26478927-26478928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26462025..26466474-chr6:26476591..26479281,4	K562	blood:
2	chr6:26472114..26481394-chr6:26482721..26495847,23	K562	blood:
3	chr6:26156637..26159551-chr6:26477996..26481463,4	K562	blood:
4	chr6:26460571..26466560-chr6:26477285..26481131,5	K562	blood:
5	chr6:26470613..26473867-chr6:26476951..26479626,4	K562	blood:
6	chr6:26476693..26479520-chr6:26480371..26483331,3	MCF-7	breast:
7	chr6:26477480..26482334-chr6:26483111..26488376,9	K562	blood:

Variant related genes	Relation type
ENSG00000158373	Chromatin interaction
ENSG00000112763	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 14 )

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	0.85[ASN][1000 genomes]
rs12176317	0.85[CEU][hapmap]
rs13195047	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13210025	0.86[JPT][hapmap]
rs13214027	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs13216828	0.85[CEU][hapmap]
rs16891717	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16891725	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.98[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2295593	0.85[ASN][1000 genomes]
rs2393657	0.86[ASN][1000 genomes]
rs2393665	0.86[ASN][1000 genomes]
rs2393667	0.85[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs34313099	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3734544	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]
rs3757150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.85[ASN][1000 genomes]
rs3999471	0.92[JPT][hapmap]
rs4518487	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4634439	0.92[JPT][hapmap]
rs56296968	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.85[ASN][1000 genomes]
rs6900118	0.89[CHB][hapmap];0.88[CHD][hapmap]
rs6900665	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6911765	1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[ASN][1000 genomes]
rs6920256	0.92[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.86[ASN][1000 genomes]
rs9348719	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348720	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348721	0.94[ASN][1000 genomes]
rs9357007	0.86[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];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.90[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];1.00[ASN][1000 genomes]
rs9358947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9358948	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.87[ASN][1000 genomes]
rs9379880	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9379882	0.85[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	0.81[ASN][1000 genomes]
rs9393727	0.85[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:6 , 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	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
5	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
6	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9358946	BTN2A1	Cis_1M	lymphoblastoid	RTeQTL
rs9358946	BTN3A2///BTN3A3	Cis_1M	lymphoblastoid	RTeQTL
rs9358946	LOC100270746	cis	lymphoblastoid	seeQTL
rs9358946	BTN3A2	cis	lung	GTEx
rs9358946	BTN3A2	cis	Whole Blood	GTEx
rs9358946	BTN3A3	cis	lymphoblastoid	seeQTL
rs9358946	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs9358946	BTN3A2	cis	Skin Sun Exposed Lower leg	GTEx
rs9358946	CMAH	cis	parietal	SCAN
rs9358946	BTN3A2	cis	Adipose Subcutaneous	GTEx
rs9358946	BTN3A2	cis	lymphoblastoid	seeQTL
rs9358946	HIST1H3A	cis	cerebellum	SCAN
rs9358946	BTN3A2	cis	Artery Tibial	GTEx
rs9358946	BTN3A2	cis	lymphoblastoid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26475200-26481800	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells	blood
3	chr6:26475400-26479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:26475400-26479800	Enhancers	Primary B cells from peripheral blood	blood
5	chr6:26475400-26480200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr6:26475600-26479200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:26475600-26479200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:26475600-26479600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:26475600-26481400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:26476000-26479000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr6:26476000-26480200	Enhancers	HepG2	liver
12	chr6:26476200-26480400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:26476600-26489200	Weak transcription	Stomach Mucosa	stomach
14	chr6:26477000-26479200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:26477600-26479600	Enhancers	Primary B cells from cord blood	blood
16	chr6:26477800-26479000	Flanking Active TSS	K562	blood
17	chr6:26477800-26479200	Enhancers	Fetal Intestine Small	intestine
18	chr6:26478000-26479200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:26478000-26479200	Enhancers	Fetal Intestine Large	intestine
20	chr6:26478000-26479800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:26478000-26482200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:26478200-26479200	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:26478200-26480000	Weak transcription	Fetal Muscle Leg	muscle
24	chr6:26478200-26481200	Weak transcription	Lung	lung
25	chr6:26478400-26479000	Enhancers	GM12878-XiMat	blood
26	chr6:26478800-26479000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr6:26478800-26485200	Weak transcription	Small Intestine	intestine

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