Variant report

Variant	rs12986653
Chromosome Location	chr2:46718090-46718091
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46713674..46717376-chr2:46717590..46719594,3	K562	blood:
2	chr2:46713674..46716471-chr2:46717649..46719594,2	K562	blood:
3	chr2:46712457..46718126-chr2:46724421..46727428,6	K562	blood:
4	chr2:46716484..46718309-chr2:46842742..46845548,2	K562	blood:

Variant related genes	Relation type
ENSG00000253515	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11125075	1.00[JPT][hapmap]
rs13001507	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13002880	0.95[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs13005507	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13007688	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]
rs13008445	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13008941	0.82[ASN][1000 genomes]
rs13010097	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13011481	1.00[YRI][hapmap]
rs13014744	0.82[EUR][1000 genomes]
rs13020043	0.84[AMR][1000 genomes]
rs13023346	0.81[EUR][1000 genomes]
rs13024277	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13024546	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13025211	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447563	0.89[JPT][hapmap]
rs1530621	0.91[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap]
rs1530628	0.84[CEU][hapmap]
rs17817004	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1900591	0.83[AMR][1000 genomes]
rs2084679	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2121698	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2122714	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2346414	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2346415	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs34854267	0.83[AMR][1000 genomes]
rs35272216	0.82[ASN][1000 genomes]
rs35509718	0.84[AMR][1000 genomes]
rs36006825	0.83[AMR][1000 genomes]
rs3754556	0.82[YRI][hapmap]
rs3768730	1.00[YRI][hapmap]
rs4312543	0.84[AMR][1000 genomes]
rs4396767	1.00[JPT][hapmap]
rs4549147	0.83[AMR][1000 genomes]
rs4952830	0.91[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs4952831	0.82[YRI][hapmap]
rs4952833	0.82[YRI][hapmap]
rs4953372	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs4953387	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4953388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953390	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4953396	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62134696	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62134698	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6544895	0.84[AMR][1000 genomes]
rs6544898	0.86[ASW][hapmap];0.91[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6749877	0.84[AMR][1000 genomes]
rs718849	0.84[AMR][1000 genomes]
rs7556828	0.80[CEU][hapmap]
rs7557190	0.86[ASW][hapmap];0.87[GIH][hapmap];0.82[YRI][hapmap]
rs7565770	0.84[CEU][hapmap]
rs7607633	0.82[YRI][hapmap]
rs880671	0.95[CEU][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv581746	chr2:46699145-46719922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv581747	chr2:46709571-46718989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	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
17	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12986653	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs12986653	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs12986653	RHOQ	cis	cerebellum	SCAN
rs12986653	CRIPT	cis	parietal	SCAN
rs12986653	CRIPT	cis	lymphoblastoid	seeQTL
rs12986653	PIGF	cis	lymphoblastoid	seeQTL
rs12986653	ATP6V1E2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46713800-46718800	Enhancers	Spleen	Spleen
2	chr2:46714600-46718400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:46714600-46718600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:46714600-46718800	Enhancers	Fetal Heart	heart
5	chr2:46714600-46718800	Enhancers	NHLF	lung
6	chr2:46714600-46719200	Enhancers	Left Ventricle	heart
7	chr2:46714800-46718600	Enhancers	Right Ventricle	heart
8	chr2:46714800-46718800	Enhancers	Adipose Nuclei	Adipose
9	chr2:46714800-46718800	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:46714800-46720800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:46714800-46721600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr2:46715200-46718800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:46715400-46718200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr2:46715400-46720400	Weak transcription	HUVEC	blood vessel
15	chr2:46715600-46718200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr2:46715600-46718200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:46715800-46719800	Weak transcription	A549	lung
18	chr2:46715800-46720400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:46716000-46718600	Enhancers	Brain Germinal Matrix	brain
20	chr2:46716200-46718200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:46716200-46718600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:46716200-46718600	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:46716200-46719000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:46716400-46718200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr2:46716400-46718400	Enhancers	Primary B cells from cord blood	blood
26	chr2:46716400-46718600	Enhancers	Fetal Brain Male	brain
27	chr2:46716400-46718800	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr2:46716400-46719000	Enhancers	Primary hematopoietic stem cells	blood
29	chr2:46716600-46718200	Enhancers	H1 Cell Line	embryonic stem cell
30	chr2:46716600-46718200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:46716600-46718200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:46716600-46718200	Enhancers	Placenta	Placenta
33	chr2:46716600-46718400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:46716600-46718400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:46716600-46718400	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr2:46716600-46718400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
37	chr2:46716600-46718400	Enhancers	Right Atrium	heart
38	chr2:46716600-46718600	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr2:46716600-46718600	Enhancers	Primary B cells from peripheral blood	blood
40	chr2:46716600-46718600	Enhancers	Brain Substantia Nigra	brain
41	chr2:46716600-46718800	Enhancers	Brain Angular Gyrus	brain
42	chr2:46716600-46718800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:46716600-46718800	Enhancers	Fetal Stomach	stomach
44	chr2:46716600-46718800	Enhancers	Fetal Thymus	thymus
45	chr2:46716600-46720400	Enhancers	GM12878-XiMat	blood
46	chr2:46716800-46718200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:46716800-46718200	Enhancers	Fetal Brain Female	brain
48	chr2:46716800-46718400	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr2:46716800-46718400	Enhancers	HSMMtube	muscle
50	chr2:46716800-46718800	Enhancers	Rectal Smooth Muscle	rectum

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