Variant report

Variant	rs13007688
Chromosome Location	chr2:46721240-46721241
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46707494..46710484-chr2:46718946..46721502,2	K562	blood:
2	chr2:46715260..46716783-chr2:46718663..46721578,2	MCF-7	breast:
3	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs12986653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13001507	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13002880	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13005507	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13008418	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs13008445	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008941	0.81[EUR][1000 genomes]
rs13010097	0.81[EUR][1000 genomes]
rs13011481	1.00[YRI][hapmap]
rs13011721	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13014744	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13020043	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13023346	0.85[EUR][1000 genomes]
rs13024277	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13024546	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13025211	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13030579	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1530621	0.91[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs1530628	0.84[CEU][hapmap]
rs17817004	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1900591	0.82[AMR][1000 genomes]
rs2121698	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2121700	1.00[JPT][hapmap]
rs2122714	0.92[EUR][1000 genomes]
rs2346414	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2346415	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs34334183	0.89[ASN][1000 genomes]
rs34854267	0.82[AMR][1000 genomes]
rs35509718	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs36006825	0.82[AMR][1000 genomes]
rs3754556	0.82[YRI][hapmap]
rs3768730	1.00[YRI][hapmap]
rs4312543	0.83[AMR][1000 genomes]
rs4549147	0.81[AMR][1000 genomes]
rs4952830	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4952831	0.82[YRI][hapmap]
rs4952833	0.82[YRI][hapmap]
rs4953372	1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4953387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953388	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4953390	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953396	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61701220	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs62134696	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62134698	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6544895	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6544898	0.86[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6749877	0.83[AMR][1000 genomes]
rs718849	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7556828	0.80[CEU][hapmap]
rs7557190	0.86[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7565770	0.84[CEU][hapmap]
rs7607633	0.82[YRI][hapmap]
rs880671	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]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv457341	chr2:46712759-46724016	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv581748	chr2:46712759-46724016	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs13007688	CRIPT	cis	parietal	SCAN
rs13007688	CRIPT	cis	lymphoblastoid	seeQTL
rs13007688	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs13007688	PIGF	cis	lymphoblastoid	seeQTL
rs13007688	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs13007688	RHOQ	cis	cerebellum	SCAN
rs13007688	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs13007688	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr2:46718000-46722600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46718200-46722600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:46718200-46726600	Weak transcription	Aorta	Aorta
5	chr2:46718400-46726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:46718600-46722000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:46718600-46722600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:46718600-46725600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:46718600-46726600	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:46718600-46726600	Weak transcription	Right Ventricle	heart
11	chr2:46718800-46722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:46718800-46726400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:46718800-46726600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:46718800-46727000	Weak transcription	Spleen	Spleen
15	chr2:46719400-46721400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:46719800-46721400	Enhancers	Fetal Heart	heart
17	chr2:46720000-46721400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:46720000-46721400	Enhancers	Hela-S3	cervix
19	chr2:46720000-46721400	Enhancers	NHLF	lung
20	chr2:46720000-46721400	Enhancers	Osteobl	bone
21	chr2:46720400-46721400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:46720400-46721400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:46720400-46721600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:46720400-46721600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:46720400-46721800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:46720400-46721800	Enhancers	Fetal Brain Female	brain
27	chr2:46720400-46722200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:46720600-46721600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr2:46720600-46722000	Enhancers	Brain Germinal Matrix	brain
30	chr2:46720600-46723400	Enhancers	Fetal Brain Male	brain
31	chr2:46720800-46721400	Enhancers	Stomach Smooth Muscle	stomach
32	chr2:46720800-46722600	Weak transcription	HSMM	muscle
33	chr2:46721000-46721400	Enhancers	NH-A	brain
34	chr2:46721000-46721600	Enhancers	Brain Anterior Caudate	brain
35	chr2:46721000-46722600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:46721000-46722600	Weak transcription	NHDF-Ad	bronchial
37	chr2:46721000-46726600	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:46721200-46721600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:46721200-46721600	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:46721200-46721600	Enhancers	GM12878-XiMat	blood
41	chr2:46721200-46721600	Enhancers	NHEK	skin
42	chr2:46721200-46722600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:46721200-46726600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:46721200-46726600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:46721200-46726600	Weak transcription	Left Ventricle	heart

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