Variant report

Variant	rs880671
Chromosome Location	chr2:46746256-46746257
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46745057..46747002-chr2:46767957..46769479,2	K562	blood:
2	chr2:46745227..46747707-chr2:46842896..46845007,2	K562	blood:

Variant related genes	Relation type
ENSG00000119878	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12470532	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs12474287	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs12986653	0.95[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13002880	0.90[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs13005507	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13007688	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008418	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008445	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008941	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13010097	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13011481	0.82[YRI][hapmap]
rs13011721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13014744	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023346	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13024277	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13024546	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13025211	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13030579	0.95[CEU][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1530621	0.86[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17817004	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084679	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2121698	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2121700	1.00[JPT][hapmap]
rs2346414	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2346415	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34334183	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35178974	0.81[AFR][1000 genomes]
rs35272216	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3768730	0.82[YRI][hapmap]
rs3814045	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4952830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952831	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4952833	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs4953372	0.82[YRI][hapmap]
rs4953387	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953388	0.95[CEU][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4953390	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4953396	0.83[EUR][1000 genomes]
rs61701220	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62134696	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62134698	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62134736	0.81[AFR][1000 genomes]
rs6544898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557190	0.90[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7607633	1.00[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs880671	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs880671	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs880671	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46733800-46753000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:46739600-46755000	Weak transcription	Aorta	Aorta
3	chr2:46743400-46758400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:46744800-46747800	Weak transcription	HSMM	muscle
5	chr2:46744800-46761800	Weak transcription	A549	lung
6	chr2:46745800-46746600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr2:46745800-46747000	Enhancers	Fetal Brain Male	brain
8	chr2:46745800-46748400	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr2:46745800-46748600	Enhancers	Adipose Nuclei	Adipose
10	chr2:46746000-46746400	Enhancers	Liver	Liver
11	chr2:46746000-46746600	Enhancers	Brain Anterior Caudate	brain
12	chr2:46746000-46746800	Enhancers	Psoas Muscle	Psoas
13	chr2:46746000-46747400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr2:46746000-46749400	Enhancers	Fetal Lung	lung
15	chr2:46746000-46749400	Enhancers	Fetal Muscle Trunk	muscle
16	chr2:46746000-46749400	Enhancers	Fetal Muscle Leg	muscle
17	chr2:46746000-46749400	Enhancers	Placenta	Placenta
18	chr2:46746000-46749400	Enhancers	Fetal Stomach	stomach
19	chr2:46746200-46746400	Enhancers	Right Ventricle	heart
20	chr2:46746200-46748400	Enhancers	Lung	lung
21	chr2:46746200-46748800	Enhancers	Left Ventricle	heart

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