Variant report

Variant	rs2074941
Chromosome Location	chr19:57060573-57060574
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11667052	0.89[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs12151151	0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs12978999	0.87[LWK][hapmap];0.82[YRI][hapmap]
rs12981980	0.87[LWK][hapmap];0.83[YRI][hapmap]
rs16987295	0.83[YRI][hapmap]
rs16987310	0.87[LWK][hapmap];0.83[YRI][hapmap]
rs2074942	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215151	0.81[YRI][hapmap]
rs2286422	0.81[AFR][1000 genomes]
rs2869891	0.80[AFR][1000 genomes]
rs3813141	0.92[LWK][hapmap];0.88[YRI][hapmap]
rs3813143	0.92[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs4801333	0.86[JPT][hapmap]
rs4801334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245557	0.80[AFR][1000 genomes]
rs7250075	0.81[YRI][hapmap]
rs7260223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110306	0.83[YRI][hapmap]
rs917407	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking 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 miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv580385	chr19:56918598-57072433	ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv1057240	chr19:56919831-57153659	Flanking Active TSS Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv544097	chr19:56919831-57153659	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv580386	chr19:56924761-57072433	Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
10	nsv1055357	chr19:56933632-57190007	ZNF genes & repeats Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
11	nsv912518	chr19:56995737-57109821	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv912519	chr19:57020754-57065189	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv1062806	chr19:57050734-57191914	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2074941	ZNF135	cis	cerebellum	SCAN
rs2074941	ZNF606	cis	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:57047400-57077800	ZNF genes & repeats	Liver	Liver
2	chr19:57050600-57062800	ZNF genes & repeats	A549	lung
3	chr19:57050800-57063000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:57050800-57067000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:57051000-57060800	ZNF genes & repeats	Primary B cells from cord blood	blood
6	chr19:57051200-57062600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
7	chr19:57051200-57068000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:57051400-57063000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:57051400-57068000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:57051400-57068000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:57051400-57068000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr19:57051400-57068000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:57051400-57070600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:57051600-57060600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:57051600-57061200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:57051600-57067200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr19:57051600-57078000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:57051800-57066600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
19	chr19:57051800-57067000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
20	chr19:57052200-57063000	ZNF genes & repeats	Fetal Brain Female	brain
21	chr19:57052200-57070200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
22	chr19:57052400-57062600	ZNF genes & repeats	Ovary	ovary
23	chr19:57052400-57068000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr19:57052600-57062800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
25	chr19:57052600-57063000	ZNF genes & repeats	Fetal Muscle Leg	muscle
26	chr19:57052600-57067800	ZNF genes & repeats	Dnd41	blood
27	chr19:57053800-57063000	ZNF genes & repeats	Fetal Lung	lung
28	chr19:57054000-57068000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:57054800-57062400	ZNF genes & repeats	Aorta	Aorta
30	chr19:57054800-57077800	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr19:57055000-57067200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr19:57055000-57070800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:57055200-57063000	ZNF genes & repeats	Brain Hippocampus Middle	brain
34	chr19:57055200-57063000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
35	chr19:57055200-57068000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
36	chr19:57056200-57063000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr19:57056200-57068000	ZNF genes & repeats	Brain Substantia Nigra	brain
38	chr19:57057000-57062600	ZNF genes & repeats	HSMM	muscle
39	chr19:57057000-57063200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
40	chr19:57058000-57062800	ZNF genes & repeats	HSMMtube	muscle
41	chr19:57058000-57063000	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr19:57058200-57068200	ZNF genes & repeats	Colon Smooth Muscle	Colon
43	chr19:57058400-57062800	ZNF genes & repeats	Brain Anterior Caudate	brain
44	chr19:57058400-57062800	ZNF genes & repeats	Colonic Mucosa	Colon
45	chr19:57058400-57062800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
46	chr19:57058400-57067200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr19:57058600-57060600	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr19:57058600-57061200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr19:57058600-57062600	ZNF genes & repeats	NH-A	brain
50	chr19:57058600-57066400	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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