Variant report

Variant	rs10407502
Chromosome Location	chr19:52735549-52735550
allele	C/T
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	POLR2A	chr19:52733968-52735570	U87	brain:	n/a	n/a
2	POLR2A	chr19:52734774-52735653	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:52733737-52735599	U87	brain:	n/a	n/a
4	POLR2A	chr19:52733795-52735686	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52714640..52717140-chr19:52734016..52736347,2	K562	blood:
2	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268015	TF binding region
ENSG00000105568	Chromatin interaction
ENSG00000196214	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1025279	1.00[JPT][hapmap]
rs10402209	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10402638	0.96[ASN][1000 genomes]
rs10403154	1.00[JPT][hapmap]
rs10403202	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10403283	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10403311	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10403464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10403806	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10404236	1.00[JPT][hapmap]
rs10404437	0.96[ASN][1000 genomes]
rs10407063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10407987	1.00[JPT][hapmap]
rs10408119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10411211	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412110	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10412196	0.92[ASN][1000 genomes]
rs10413012	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10413435	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414083	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414197	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10414423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414536	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414852	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10416785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10417253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10417820	1.00[JPT][hapmap]
rs10418666	0.83[ASN][1000 genomes]
rs10419304	1.00[JPT][hapmap]
rs10420207	0.85[ASN][1000 genomes]
rs10420254	1.00[JPT][hapmap]
rs10420560	0.96[ASN][1000 genomes]
rs10421440	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10421589	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10422483	0.82[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10422838	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423125	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10423610	1.00[JPT][hapmap]
rs10423794	1.00[JPT][hapmap]
rs10424348	1.00[JPT][hapmap]
rs10425135	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10426002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10426066	1.00[JPT][hapmap]
rs10426786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1056348	1.00[JPT][hapmap]
rs11879419	1.00[JPT][hapmap]
rs13344984	1.00[JPT][hapmap]
rs16983548	1.00[JPT][hapmap]
rs16983549	1.00[JPT][hapmap]
rs16983557	1.00[JPT][hapmap]
rs16983598	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16983601	0.96[ASN][1000 genomes]
rs16983603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16983610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17835942	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2115074	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288409	1.00[JPT][hapmap]
rs2288410	1.00[JPT][hapmap]
rs2303685	1.00[JPT][hapmap]
rs2560871	1.00[JPT][hapmap]
rs28444225	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs28563055	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4458121	1.00[JPT][hapmap]
rs55751302	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55871532	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57102373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60063830	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6509628	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7249460	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs7255058	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7255677	0.82[ASN][1000 genomes]
rs7255737	1.00[CHB][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7256125	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7256216	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7256300	1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7256312	1.00[CHB][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7256719	1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7259175	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs73935052	0.96[ASN][1000 genomes]
rs73935053	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755531	1.00[JPT][hapmap]
rs8100048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8100600	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs8101990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8103874	1.00[JPT][hapmap]
rs8105432	0.96[ASN][1000 genomes]
rs8106271	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes]
rs8106544	0.90[ASN][1000 genomes]
rs8107377	1.00[JPT][hapmap]
rs8108636	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8109061	0.80[ASN][1000 genomes]
rs8109512	0.96[ASN][1000 genomes]
rs8110857	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8110881	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs874421	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers 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 miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:52731000-52736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr19:52731000-52736800	Weak transcription	Stomach Mucosa	stomach
6	chr19:52731600-52736400	Weak transcription	Fetal Heart	heart
7	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
8	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:52731800-52736600	Weak transcription	HUVEC	blood vessel
10	chr19:52732000-52736000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr19:52732000-52736000	Weak transcription	Psoas Muscle	Psoas
12	chr19:52732000-52736600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:52732200-52735600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr19:52732200-52736000	Weak transcription	Ovary	ovary
17	chr19:52732200-52736000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr19:52732200-52736200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:52732200-52736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:52732200-52741000	Weak transcription	Dnd41	blood
21	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
22	chr19:52732400-52735800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:52732400-52735800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr19:52732400-52735800	Weak transcription	Left Ventricle	heart
25	chr19:52732400-52736000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:52732400-52736000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr19:52732400-52736400	Weak transcription	Adipose Nuclei	Adipose
28	chr19:52732400-52737800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr19:52732400-52737800	Weak transcription	HepG2	liver
30	chr19:52732400-52740200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:52732400-52740600	Weak transcription	Brain Angular Gyrus	brain
32	chr19:52732400-52741000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr19:52732400-52741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr19:52732600-52736000	Weak transcription	Spleen	Spleen
35	chr19:52732600-52736400	Weak transcription	Fetal Brain Female	brain
36	chr19:52732600-52736800	Weak transcription	Primary T cells from cord blood	blood
37	chr19:52733000-52735600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr19:52733000-52736000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:52733000-52736200	Weak transcription	Thymus	Thymus
40	chr19:52733000-52736600	Weak transcription	Fetal Intestine Large	intestine
41	chr19:52733000-52736600	Weak transcription	HSMM	muscle
42	chr19:52733000-52736800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:52733000-52737000	Weak transcription	Placenta	Placenta
44	chr19:52733000-52737400	Weak transcription	Colonic Mucosa	Colon
45	chr19:52733200-52735600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr19:52733200-52736400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:52733200-52736600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr19:52733200-52742800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:52733200-52759600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:52733400-52741200	Weak transcription	Fetal Muscle Trunk	muscle

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