Variant report

Variant	rs12105006
Chromosome Location	chr2:46862586-46862587
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46854125..46858531-chr2:46860398..46864023,5	K562	blood:
2	chr2:46845600..46848148-chr2:46860947..46862599,2	K562	blood:
3	chr2:46861539..46864465-chr2:46873004..46877415,5	MCF-7	breast:
4	chr2:46845764..46848148-chr2:46860387..46862849,3	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10495934	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs13000706	0.81[CHD][hapmap]
rs13024534	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531133	0.81[CHD][hapmap]
rs17767994	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17768018	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17768132	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17768138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17818399	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17819022	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1869836	0.81[ASN][1000 genomes]
rs2122715	0.84[CHD][hapmap]
rs2346419	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3087822	0.85[CHD][hapmap]
rs34449783	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34748737	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34752561	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34996358	0.85[EUR][1000 genomes]
rs35837037	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35909669	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35949012	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4952836	0.86[ASN][1000 genomes]
rs4952837	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62136873	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62136894	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6544909	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs6746598	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7560464	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs896212	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs982395	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
4	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
5	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
6	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
7	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
9	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12105006	CRIPT	cis	multi-tissue	Pritchard
rs12105006	CRIPT	cis	Temporal Cortex	GTEx
rs12105006	SOCS5	cis	multi-tissue	Pritchard
rs12105006	CRIPT	cis	Frontal Cortex	GTEx
rs12105006	CRIPT	Cis_1M	lymphoblastoid	RTeQTL
rs12105006	PIGF	cis	parietal	SCAN
rs12105006	CRIPT	cis	parietal	SCAN
rs12105006	ATP6V1E2	cis	Muscle Skeletal	GTEx
rs12105006	CRIPT	cis	lymphoblastoid	seeQTL
rs12105006	ATP6V1E2	cis	parietal	SCAN
rs12105006	ATP6V1E2	cis	Heart Left Ventricle	GTEx
rs12105006	PIGF	cis	lymphoblastoid	seeQTL
rs12105006	ATP6V1E2	cis	multi-tissue	Pritchard
rs12105006	ATP6V1E2	cis	lymphoblastoid	seeQTL
rs12105006	CRIPT	cis	Artery Tibial	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46844800-46865600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:46844800-46868400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:46844800-46868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46844800-46868800	Weak transcription	Esophagus	oesophagus
5	chr2:46844800-46872200	Weak transcription	Pancreas	Pancrea
6	chr2:46845400-46864800	Weak transcription	Psoas Muscle	Psoas
7	chr2:46845400-46867000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:46845400-46871000	Weak transcription	Stomach Mucosa	stomach
9	chr2:46845400-46873000	Weak transcription	Right Ventricle	heart
10	chr2:46845600-46868200	Weak transcription	Aorta	Aorta
11	chr2:46845600-46868800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr2:46846000-46868600	Weak transcription	Fetal Intestine Small	intestine
13	chr2:46848600-46864800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:46848600-46867400	Weak transcription	Lung	lung
15	chr2:46848600-46871200	Weak transcription	HSMMtube	muscle
16	chr2:46848600-46872600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:46848600-46872800	Weak transcription	Left Ventricle	heart
18	chr2:46848600-46872800	Weak transcription	Ovary	ovary
19	chr2:46848800-46868000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr2:46848800-46871000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:46848800-46872600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:46848800-46873000	Weak transcription	Brain Angular Gyrus	brain
23	chr2:46849000-46868600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr2:46849000-46868600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr2:46849000-46877200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:46849200-46869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:46849200-46869800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:46849200-46870800	Weak transcription	Hela-S3	cervix
29	chr2:46849200-46872600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:46849400-46872800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:46849800-46868200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:46850200-46868400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:46851600-46867600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:46852000-46868200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:46852000-46872800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:46852400-46869400	Weak transcription	Dnd41	blood
37	chr2:46853400-46865600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr2:46853400-46869600	Weak transcription	Brain Germinal Matrix	brain
39	chr2:46853400-46872600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:46853400-46872800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:46853600-46868600	Weak transcription	Fetal Intestine Large	intestine
42	chr2:46853600-46869400	Weak transcription	NH-A	brain
43	chr2:46853800-46863800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr2:46853800-46864000	Weak transcription	Fetal Brain Female	brain
45	chr2:46853800-46864800	Weak transcription	HSMM	muscle
46	chr2:46853800-46865400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:46853800-46868000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:46853800-46868600	Weak transcription	Primary B cells from cord blood	blood
49	chr2:46853800-46868800	Weak transcription	Placenta	Placenta
50	chr2:46853800-46873000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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