Variant report

Variant	rs2945988
Chromosome Location	chr19:37010552-37010553
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37005079..37007433-chr19:37008961..37011612,3	K562	blood:
2	chr19:37008017..37010772-chr19:37018818..37020812,2	K562	blood:

Variant related genes	Relation type
ENSG00000254004	Chromatin interaction
ENSG00000228629	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1878927	0.93[JPT][hapmap];0.88[YRI][hapmap]
rs2052730	0.85[ASN][1000 genomes]
rs2385796	0.90[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs2912420	0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs2912422	0.82[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs2912424	0.85[ASN][1000 genomes]
rs2912426	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912427	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2912428	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912431	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912434	0.88[ASN][1000 genomes]
rs2912436	0.87[ASN][1000 genomes]
rs2912437	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs2912438	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945946	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2945960	0.86[ASN][1000 genomes]
rs2945966	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945967	0.87[ASN][1000 genomes]
rs2945968	0.85[ASN][1000 genomes]
rs2945970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2945974	0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2945977	0.85[ASN][1000 genomes]
rs2945979	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2945980	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2945982	0.91[ASN][1000 genomes]
rs2945987	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967432	0.93[AFR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967434	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2967435	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2967441	0.87[ASN][1000 genomes]
rs2967448	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2967449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2967450	0.89[CHB][hapmap];0.93[ASN][1000 genomes]
rs2967451	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2967452	0.84[ASN][1000 genomes]
rs2967456	0.88[CEU][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967457	0.85[ASN][1000 genomes]
rs2967467	0.81[ASN][1000 genomes]
rs2967468	0.83[ASN][1000 genomes]
rs2967471	0.84[ASN][1000 genomes]
rs2967474	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967475	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967505	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2967532	0.94[JPT][hapmap];0.93[YRI][hapmap]
rs2967533	0.94[JPT][hapmap];0.93[YRI][hapmap]
rs2967542	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2967544	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3107237	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3107238	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3111554	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4561584	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2945988	CADM4	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36999200-37014400	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:36999200-37018000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:36999800-37017400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:37000000-37011600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:37000000-37016400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:37000000-37017000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37000000-37017800	ZNF genes & repeats	Liver	Liver
8	chr19:37001000-37018000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:37001400-37010600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:37001400-37017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:37001600-37016400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:37001600-37018200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:37002400-37014000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:37002400-37014200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
15	chr19:37002600-37012400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:37002600-37018000	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:37002800-37016400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:37002800-37016800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr19:37003200-37014400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
20	chr19:37003200-37014400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr19:37003200-37016800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37003200-37017000	ZNF genes & repeats	Fetal Lung	lung
23	chr19:37003200-37018000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
24	chr19:37003400-37016800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
25	chr19:37003400-37017000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr19:37003400-37017200	ZNF genes & repeats	Dnd41	blood
27	chr19:37003400-37017400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
28	chr19:37003600-37012200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
29	chr19:37003600-37012600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:37003600-37014400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
31	chr19:37003800-37017000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr19:37003800-37018200	ZNF genes & repeats	Brain Germinal Matrix	brain
33	chr19:37003800-37018600	ZNF genes & repeats	A549	lung
34	chr19:37004200-37010600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
35	chr19:37004200-37014400	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr19:37004200-37015000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
37	chr19:37004400-37010800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
38	chr19:37004400-37012400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr19:37004400-37014600	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr19:37004600-37010600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
41	chr19:37004600-37010600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
42	chr19:37004600-37014400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:37004600-37016400	Strong transcription	Placenta Amnion	Placenta Amnion
44	chr19:37004600-37016600	ZNF genes & repeats	Fetal Muscle Leg	muscle
45	chr19:37004600-37017400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:37004800-37010600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
47	chr19:37004800-37016600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr19:37005000-37014400	ZNF genes & repeats	GM12878-XiMat	blood
49	chr19:37005000-37016400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
50	chr19:37005000-37016800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland

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