Variant report

Variant	rs6510999
Chromosome Location	chr19:18847832-18847833
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18841664..18844325-chr19:18846428..18848606,2	MCF-7	breast:
2	chr19:18845794..18848045-chr19:18852674..18855660,3	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:30)

rs_ID	r²[population]
rs12984991	0.98[ASN][1000 genomes]
rs17757406	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2075017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240014	0.82[GIH][hapmap];0.85[TSI][hapmap]
rs2240887	0.89[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808154	0.96[ASN][1000 genomes]
rs4808851	0.95[ASN][1000 genomes]
rs4808852	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808853	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56182405	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56210931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57962499	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58406187	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61447117	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6510997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6510998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511000	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6511001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71332136	0.94[ASN][1000 genomes]
rs71332137	0.98[ASN][1000 genomes]
rs71332138	0.98[ASN][1000 genomes]
rs7251560	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251710	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252217	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7256502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257846	0.85[TSI][hapmap]
rs7258259	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73537985	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73537994	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73537995	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:3 , 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

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18821200-18860600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr19:18821200-18861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr19:18821200-18864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr19:18827600-18860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:18828800-18850400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:18829200-18860000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr19:18829200-18861400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr19:18833800-18853400	Weak transcription	Primary T cells from cord blood	blood
9	chr19:18833800-18860400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr19:18833800-18860800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr19:18835000-18860600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:18835200-18853200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:18841200-18852000	Weak transcription	Small Intestine	intestine
14	chr19:18842000-18848400	Enhancers	Fetal Muscle Leg	muscle
15	chr19:18842200-18853400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:18842600-18851000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:18842600-18853400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr19:18842800-18856600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:18842800-18861000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:18843000-18860600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr19:18843800-18848400	Enhancers	Placenta	Placenta
22	chr19:18844200-18872800	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr19:18844400-18848200	Enhancers	Fetal Heart	heart
24	chr19:18844400-18848600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:18844400-18859800	Weak transcription	Fetal Brain Female	brain
26	chr19:18844400-18867400	Weak transcription	HSMMtube	muscle
27	chr19:18844600-18848200	Weak transcription	Fetal Kidney	kidney
28	chr19:18844600-18851800	Weak transcription	Right Atrium	heart
29	chr19:18844600-18852000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr19:18844600-18860600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr19:18844600-18872800	Weak transcription	NH-A	brain
32	chr19:18844800-18851200	Weak transcription	Left Ventricle	heart
33	chr19:18844800-18852200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr19:18844800-18852600	Weak transcription	Ovary	ovary
35	chr19:18844800-18871800	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:18845000-18848200	Weak transcription	K562	blood
37	chr19:18845000-18852000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:18845200-18848200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr19:18845400-18848000	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr19:18845600-18854200	Weak transcription	NHLF	lung
41	chr19:18845800-18848000	Enhancers	Brain Angular Gyrus	brain
42	chr19:18845800-18848600	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr19:18845800-18849000	Enhancers	Brain Anterior Caudate	brain
44	chr19:18846000-18850000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr19:18846000-18864200	Weak transcription	Primary B cells from cord blood	blood
46	chr19:18846400-18850200	Enhancers	Gastric	stomach
47	chr19:18846600-18848200	Enhancers	Esophagus	oesophagus
48	chr19:18846600-18850400	Enhancers	Pancreas	Pancrea
49	chr19:18846600-18852000	Enhancers	Stomach Mucosa	stomach
50	chr19:18846600-18855000	Enhancers	Fetal Intestine Large	intestine

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