Variant report

Variant	rs6795301
Chromosome Location	chr3:141754558-141754559
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141750870..141754798-chr3:141761535..141764566,4	K562	blood:
2	chr3:141743469..141745043-chr3:141753876..141755747,2	K562	blood:
3	chr3:141748723..141752115-chr3:141753472..141758138,4	MCF-7	breast:
4	chr3:141751486..141755736-chr3:141759507..141766558,8	K562	blood:
5	chr3:141745791..141750569-chr3:141753730..141757585,7	K562	blood:
6	chr3:141752908..141754951-chr3:141758367..141761126,3	K562	blood:

Variant related genes	Relation type
ENSG00000233597	Chromatin interaction
ENSG00000114126	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10755098	1.00[LWK][hapmap]
rs10935453	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs11569198	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11569216	0.94[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs11706480	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs12495978	0.94[CHB][hapmap];0.92[ASN][1000 genomes]
rs13069749	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1355438	0.82[JPT][hapmap]
rs1397764	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs1543064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851892	1.00[LWK][hapmap]
rs1704990	0.80[AMR][1000 genomes]
rs1705612	0.83[CHB][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap]
rs1705613	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs1705619	0.80[AMR][1000 genomes]
rs1820941	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2063453	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2063454	1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2271386	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2861422	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs2862122	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2862123	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2862124	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2862125	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2862126	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34092379	0.88[ASN][1000 genomes]
rs34464850	0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34486172	0.88[ASN][1000 genomes]
rs34514405	0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34579489	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347684	0.82[ASN][1000 genomes]
rs347688	0.80[AMR][1000 genomes]
rs347689	0.84[ASN][1000 genomes]
rs347690	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35486283	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35787200	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3792411	1.00[LWK][hapmap]
rs3811708	0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs3817176	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4315664	0.86[ASN][1000 genomes]
rs4315665	0.86[ASN][1000 genomes]
rs4683417	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683669	1.00[LWK][hapmap]
rs56129773	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62283132	0.92[ASN][1000 genomes]
rs6764833	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791514	0.82[JPT][hapmap]
rs6795500	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803884	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806443	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7426584	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7611705	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs7619506	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630837	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633321	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7638352	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7644383	0.88[CHB][hapmap];0.82[JPT][hapmap]
rs907293	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289641	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs963396	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9848817	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9863685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9865777	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.80[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9877536	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs9880805	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv2757892	chr3:141728870-142129836	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	esv2759182	chr3:141728870-142129836	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv877553	chr3:141732321-141786073	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv877554	chr3:141735532-141781890	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv877555	chr3:141740076-141791408	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6795301	ATP1B3	cis	cerebellum	SCAN
rs6795301	PLSCR1	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141747600-141762600	Weak transcription	Fetal Muscle Leg	muscle
2	chr3:141747600-141762800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:141747600-141773000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:141747600-141780400	Weak transcription	Left Ventricle	heart
5	chr3:141748200-141755200	Weak transcription	Aorta	Aorta
6	chr3:141748800-141758400	Weak transcription	Thymus	Thymus
7	chr3:141751200-141756200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:141751200-141765000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr3:141751400-141756200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:141751400-141759600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:141751400-141764400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:141752400-141759800	Weak transcription	Dnd41	blood
13	chr3:141753600-141768400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:141753800-141755800	Strong transcription	Fetal Thymus	thymus
15	chr3:141754200-141754800	Enhancers	K562	blood

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