Variant report

Variant	rs2435002
Chromosome Location	chr19:22009182-22009183
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr19:22009014-22009193	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr19:22009031-22009191	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000268438	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1510964	1.00[YRI][hapmap]
rs1543048	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998303	1.00[CHB][hapmap]
rs16998391	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998411	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998413	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2203944	1.00[CHB][hapmap]
rs2244041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2359707	1.00[ASN][1000 genomes]
rs2435001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435005	1.00[CEU][hapmap];1.00[CHB][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]
rs2435007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2435041	1.00[YRI][hapmap]
rs2435044	1.00[YRI][hapmap]
rs2435045	1.00[CEU][hapmap];1.00[CHB][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]
rs2435046	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457783	1.00[CEU][hapmap];1.00[CHB][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]
rs2457785	0.88[YRI][hapmap]
rs2457786	0.83[EUR][1000 genomes]
rs2457787	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457790	1.00[CEU][hapmap];1.00[CHB][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]
rs2457791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457793	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457795	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2457799	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4467196	1.00[CHB][hapmap]
rs6511296	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
10	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
11	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
12	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
13	nsv961194	chr19:21998424-22019912	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
14	nsv911430	chr19:22008229-22106951	ZNF genes & repeats Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription 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

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21985600-22011000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:21988600-22018000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:21988800-22017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:21989800-22013000	ZNF genes & repeats	Brain Germinal Matrix	brain
5	chr19:21990800-22017600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr19:21991200-22010800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:21995000-22016600	Weak transcription	K562	blood
8	chr19:21999800-22009400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr19:21999800-22018200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:22000800-22018200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr19:22000800-22018200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr19:22001000-22012600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr19:22001000-22014000	Weak transcription	Psoas Muscle	Psoas
14	chr19:22001000-22018000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:22001000-22018000	Weak transcription	Brain Anterior Caudate	brain
16	chr19:22001000-22018000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr19:22001200-22009200	Weak transcription	Pancreas	Pancrea
18	chr19:22001200-22018200	Weak transcription	Gastric	stomach
19	chr19:22001400-22009200	Weak transcription	Spleen	Spleen
20	chr19:22001400-22012600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:22002000-22014600	Weak transcription	NHLF	lung
22	chr19:22002000-22017800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:22002600-22018000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:22004000-22014000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:22004000-22015000	ZNF genes & repeats	Dnd41	blood
26	chr19:22004000-22015800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
27	chr19:22004000-22017600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
28	chr19:22004000-22017800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:22004200-22010200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:22004200-22010400	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr19:22004800-22014600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:22005800-22009400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:22006000-22009400	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:22006200-22009200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:22006200-22010800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:22006200-22010800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
37	chr19:22006200-22011400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:22006200-22013000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:22006200-22013000	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr19:22006400-22009400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:22006400-22009800	ZNF genes & repeats	Thymus	Thymus
42	chr19:22006400-22010800	Strong transcription	Fetal Lung	lung
43	chr19:22006400-22014800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:22006600-22009600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:22006800-22009600	ZNF genes & repeats	Lung	lung
46	chr19:22006800-22010000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr19:22006800-22010200	Strong transcription	Primary B cells from peripheral blood	blood
48	chr19:22006800-22010600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr19:22006800-22011000	ZNF genes & repeats	Fetal Brain Female	brain
50	chr19:22007000-22009400	ZNF genes & repeats	NH-A	brain

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