Variant report

Variant	rs2912438
Chromosome Location	chr19:37026443-37026444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37020966..37023894-chr19:37025965..37028005,2	K562	blood:
2	chr19:37026011..37027946-chr19:37031327..37033771,2	K562	blood:
3	chr19:37019843..37021429-chr19:37026140..37028875,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1878927	0.93[JPT][hapmap];0.88[YRI][hapmap]
rs2385796	0.94[JPT][hapmap]
rs2912420	0.94[JPT][hapmap];0.82[MKK][hapmap]
rs2912422	0.90[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs2912426	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2912427	0.88[AMR][1000 genomes]
rs2912428	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912431	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912434	0.82[ASN][1000 genomes]
rs2912436	0.92[ASN][1000 genomes]
rs2912437	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2945946	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap]
rs2945966	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2945967	0.92[ASN][1000 genomes]
rs2945968	0.89[ASN][1000 genomes]
rs2945970	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2945974	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2945979	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[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];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945980	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2945982	0.83[ASN][1000 genomes]
rs2945987	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2945988	0.94[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967432	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2967434	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2967435	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs2967441	0.92[ASN][1000 genomes]
rs2967448	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967449	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2967450	0.86[ASN][1000 genomes]
rs2967451	0.88[CHB][hapmap];0.87[JPT][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967452	0.88[ASN][1000 genomes]
rs2967456	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967468	0.83[EUR][1000 genomes]
rs2967474	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967475	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2967505	0.90[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs2967532	0.94[JPT][hapmap];0.93[YRI][hapmap]
rs2967533	0.94[JPT][hapmap];0.93[YRI][hapmap]
rs2967542	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2967544	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3107237	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3107238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111554	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4561584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2912438	ZNF225	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37020400-37034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37020600-37027600	Weak transcription	Hela-S3	cervix
3	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
4	chr19:37021600-37030000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37023200-37027000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:37023200-37031800	ZNF genes & repeats	A549	lung
9	chr19:37023200-37032600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:37023200-37048400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
12	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:37023400-37030000	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr19:37023400-37030200	ZNF genes & repeats	Fetal Intestine Small	intestine
15	chr19:37023400-37048800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
17	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
18	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
19	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
20	chr19:37023800-37033000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:37023800-37057800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr19:37023800-37058200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr19:37023800-37058200	ZNF genes & repeats	Dnd41	blood
24	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:37024000-37027000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr19:37024000-37030600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
27	chr19:37024600-37026600	ZNF genes & repeats	Brain Hippocampus Middle	brain
28	chr19:37024600-37027000	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr19:37025400-37030200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
30	chr19:37025400-37052400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
31	chr19:37025600-37026600	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
32	chr19:37025600-37026600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
33	chr19:37025600-37026600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr19:37025600-37026800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
35	chr19:37025600-37027000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
36	chr19:37025600-37027200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:37025600-37027600	Strong transcription	NHDF-Ad	bronchial
38	chr19:37025600-37027800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:37025600-37028000	ZNF genes & repeats	Brain Substantia Nigra	brain
40	chr19:37025600-37029600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
41	chr19:37025600-37030600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr19:37025600-37032800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
43	chr19:37025600-37049000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
44	chr19:37025600-37053000	ZNF genes & repeats	Brain Anterior Caudate	brain
45	chr19:37025600-37061000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
46	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr19:37025800-37026600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:37025800-37026600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
49	chr19:37025800-37026600	ZNF genes & repeats	Colonic Mucosa	Colon
50	chr19:37025800-37026600	ZNF genes & repeats	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links