Variant report

Variant	rs10405397
Chromosome Location	chr19:21994892-21994893
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10401527	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10402133	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404047	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407885	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10409170	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10409809	0.93[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs10410478	0.87[YRI][hapmap]
rs10411552	0.85[EUR][1000 genomes]
rs10411895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10413659	1.00[YRI][hapmap]
rs10413799	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs10414913	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs10415147	0.86[CEU][hapmap]
rs10425897	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10426205	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085496	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11667835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672034	0.80[YRI][hapmap]
rs11673111	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11673116	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710188	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12710191	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12973647	0.86[ASN][1000 genomes]
rs12985290	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3935082	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3935083	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7253749	0.85[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3441368	chr19:21781459-22182822	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3339694	chr19:21781479-22182792	Enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1063115	chr19:21782104-22528039	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv458525	chr19:21796943-22019697	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv578969	chr19:21796943-22019697	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv911424	chr19:21798441-22471156	Strong transcription Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv911425	chr19:21841379-22338142	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv833784	chr19:21902647-22037153	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1059457	chr19:21940891-21999025	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1059079	chr19:21940891-22083420	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv578971	chr19:21950337-22008229	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3395280	chr19:21968753-22202288	Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv911428	chr19:21986292-22106951	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv911429	chr19:21986292-22110219	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10405397	RP11-420K14.3	cis	Muscle Skeletal	GTEx
rs10405397	RP11-420K14.3	cis	lung	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21985400-22003000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:21985600-22011000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:21986200-21998800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:21987800-22002800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr19:21988600-22001000	ZNF genes & repeats	Dnd41	blood
6	chr19:21988600-22018000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:21988800-22002400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21988800-22002600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:21988800-22003000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr19:21988800-22017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:21989000-22001000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:21989000-22001600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:21989200-22000600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr19:21989400-21999200	ZNF genes & repeats	Adipose Nuclei	Adipose
15	chr19:21989600-21997400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:21989600-22002400	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:21989600-22002800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
18	chr19:21989600-22002800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
19	chr19:21989800-21997400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr19:21989800-22002200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
21	chr19:21989800-22013000	ZNF genes & repeats	Brain Germinal Matrix	brain
22	chr19:21990000-21998000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
23	chr19:21990000-22000600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:21990000-22002600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
25	chr19:21990000-22005200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr19:21990200-21997200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:21990200-21997200	ZNF genes & repeats	Fetal Lung	lung
28	chr19:21990200-22001800	ZNF genes & repeats	Primary T cells from cord blood	blood
29	chr19:21990400-21995000	ZNF genes & repeats	Fetal Kidney	kidney
30	chr19:21990400-21995400	ZNF genes & repeats	Brain Anterior Caudate	brain
31	chr19:21990400-22002800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:21990400-22002800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
33	chr19:21990600-21997800	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr19:21990800-22001600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr19:21990800-22002200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
36	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
37	chr19:21991000-21997800	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr19:21991000-22001000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
39	chr19:21991000-22002600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
40	chr19:21991000-22003800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
41	chr19:21991200-21997800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
42	chr19:21991200-21999000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:21991200-22001600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
44	chr19:21991200-22002000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr19:21991200-22002400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
46	chr19:21991200-22002600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr19:21991200-22010800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr19:21991400-21995400	ZNF genes & repeats	Colon Smooth Muscle	Colon
49	chr19:21991400-21997400	ZNF genes & repeats	Ovary	ovary
50	chr19:21991400-21997600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

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