Variant report

Variant	rs10402536
Chromosome Location	chr19:18800859-18800860
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18794491..18797092-chr19:18797337..18802619,5	K562	blood:
2	chr19:18799599..18801224-chr19:18802072..18804635,2	K562	blood:
3	chr19:18791491..18794469-chr19:18796849..18800884,3	K562	blood:
4	chr19:18793337..18796980-chr19:18797537..18801311,4	K562	blood:
5	chr19:18791530..18793331-chr19:18799550..18802078,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10403231	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10423102	0.90[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10423271	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423676	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10423852	0.89[ASN][1000 genomes]
rs1076234	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1076235	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11085237	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11085239	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668617	0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12052075	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12610845	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12974161	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12974777	0.89[ASN][1000 genomes]
rs12976741	0.89[ASN][1000 genomes]
rs12980154	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12983476	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1473115	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014914	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34143665	0.89[ASN][1000 genomes]
rs34190814	0.89[ASN][1000 genomes]
rs3795026	0.92[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4808146	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808841	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4808842	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71332133	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs889362	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs889363	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][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	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18795400-18809000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:18795400-18810800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:18795400-18811400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:18795400-18811400	Weak transcription	NH-A	brain
5	chr19:18795600-18802200	Weak transcription	Fetal Stomach	stomach
6	chr19:18795600-18802400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:18795600-18810000	Weak transcription	Thymus	Thymus
8	chr19:18795600-18810800	Weak transcription	Ovary	ovary
9	chr19:18795800-18801000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr19:18795800-18806800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr19:18795800-18807000	Weak transcription	Pancreas	Pancrea
12	chr19:18795800-18807200	Weak transcription	Esophagus	oesophagus
13	chr19:18795800-18807800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr19:18795800-18807800	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:18795800-18807800	Weak transcription	Right Ventricle	heart
16	chr19:18795800-18808400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr19:18795800-18808800	Weak transcription	Spleen	Spleen
18	chr19:18795800-18809400	Weak transcription	Primary B cells from cord blood	blood
19	chr19:18795800-18809400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:18795800-18809800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:18795800-18810600	Weak transcription	Brain Hippocampus Middle	brain
22	chr19:18795800-18810600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr19:18795800-18810800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr19:18795800-18811000	Weak transcription	Fetal Intestine Large	intestine
25	chr19:18795800-18811400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr19:18795800-18811400	Weak transcription	Fetal Lung	lung
27	chr19:18795800-18811400	Weak transcription	Right Atrium	heart
28	chr19:18796000-18802800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:18796000-18808600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr19:18796000-18809000	Weak transcription	Primary T cells from cord blood	blood
31	chr19:18796000-18809600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:18796200-18810600	Weak transcription	Brain Anterior Caudate	brain
33	chr19:18796200-18811200	Weak transcription	Fetal Brain Female	brain
34	chr19:18796600-18805200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr19:18796600-18806800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr19:18796600-18807800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr19:18796600-18810800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr19:18797200-18806000	Strong transcription	Fetal Intestine Small	intestine
39	chr19:18797200-18810600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr19:18797200-18811200	Weak transcription	NHLF	lung
41	chr19:18797200-18822400	Weak transcription	HepG2	liver
42	chr19:18797600-18808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:18797800-18809800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:18798400-18805600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:18798400-18807800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr19:18798400-18810800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:18798600-18802600	Weak transcription	Lung	lung
48	chr19:18798600-18806800	Weak transcription	Gastric	stomach
49	chr19:18798600-18807800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr19:18798800-18801400	Weak transcription	Monocytes-CD14+_RO01746	blood

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