Variant report

Variant	rs2912437
Chromosome Location	chr19:37024770-37024771
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37017700..37019947-chr19:37023301..37025958,2	K562	blood:
2	chr19:37024321..37026162-chr19:37046669..37049079,2	K562	blood:

Variant related genes	Relation type
ENSG00000254004	Chromatin interaction
ENSG00000228629	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs17206393	0.83[GIH][hapmap]
rs2052730	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2385796	0.81[JPT][hapmap]
rs2385797	0.81[MEX][hapmap]
rs2912420	0.81[JPT][hapmap]
rs2912422	0.90[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap]
rs2912424	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2912426	0.81[ASN][1000 genomes]
rs2912428	0.90[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2912431	0.83[ASN][1000 genomes]
rs2912434	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2912436	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2912438	0.92[ASN][1000 genomes]
rs2912441	0.83[GIH][hapmap]
rs2912445	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2945946	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2945960	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2945965	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945966	0.92[ASN][1000 genomes]
rs2945967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945968	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945970	0.90[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs2945974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2945977	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945979	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2945982	0.80[ASN][1000 genomes]
rs2945987	0.80[ASN][1000 genomes]
rs2945988	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2967434	0.80[ASN][1000 genomes]
rs2967435	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967448	0.84[ASN][1000 genomes]
rs2967449	0.88[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967450	0.90[CEU][hapmap];0.92[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967451	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2967452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967456	0.81[ASN][1000 genomes]
rs2967457	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2967462	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967471	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2967474	0.81[ASN][1000 genomes]
rs2967505	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967532	0.81[JPT][hapmap]
rs2967533	0.81[JPT][hapmap]
rs2967539	0.81[GIH][hapmap]
rs2967540	0.81[GIH][hapmap]
rs2967544	0.90[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs3107237	0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs3107238	0.92[ASN][1000 genomes]
rs3111554	0.87[ASN][1000 genomes]
rs4561584	0.87[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	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
6	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
9	nsv1056134	chr19:37022039-37056943	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2912437	IL29	cis	parietal	SCAN
rs2912437	KCNK6	cis	cerebellum	SCAN
rs2912437	NFKBIB	cis	parietal	SCAN
rs2912437	MRPS12	cis	parietal	SCAN
rs2912437	PRR19	cis	cerebellum	SCAN
rs2912437	PPP1R14A	cis	cerebellum	SCAN
rs2912437	ARHGEF1	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37020400-37025600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:37020400-37025600	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:37020400-37025800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:37020400-37025800	Weak transcription	Fetal Kidney	kidney
5	chr19:37020400-37025800	Weak transcription	Stomach Mucosa	stomach
6	chr19:37020400-37025800	Weak transcription	HSMM	muscle
7	chr19:37020400-37025800	Weak transcription	HSMMtube	muscle
8	chr19:37020400-37026000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr19:37020400-37034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:37020600-37025600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr19:37020600-37025800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:37020600-37025800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:37020600-37025800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:37020600-37025800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr19:37020600-37025800	Weak transcription	Placenta	Placenta
16	chr19:37020600-37025800	Weak transcription	Right Ventricle	heart
17	chr19:37020600-37027600	Weak transcription	Hela-S3	cervix
18	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
19	chr19:37021600-37030000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
20	chr19:37022600-37025400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
22	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr19:37023200-37025000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr19:37023200-37025000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:37023200-37027000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:37023200-37031800	ZNF genes & repeats	A549	lung
27	chr19:37023200-37032600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:37023200-37048400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
30	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:37023400-37024800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:37023400-37030000	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr19:37023400-37030200	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr19:37023400-37048800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
36	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
37	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr19:37023600-37024800	ZNF genes & repeats	Primary T cells from cord blood	blood
39	chr19:37023600-37024800	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr19:37023600-37024800	ZNF genes & repeats	Ovary	ovary
41	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
42	chr19:37023800-37024800	ZNF genes & repeats	Brain Substantia Nigra	brain
43	chr19:37023800-37024800	ZNF genes & repeats	NHDF-Ad	bronchial
44	chr19:37023800-37025000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr19:37023800-37033000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr19:37023800-37057800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:37023800-37058200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:37023800-37058200	ZNF genes & repeats	Dnd41	blood
49	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:37024000-37024800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain

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