Variant report

Variant	rs6508733
Chromosome Location	chr19:38000548-38000549
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37997254..37999727-chr19:37999821..38001808,2	MCF-7	breast:
2	chr19:37996541..38000346-chr19:38000524..38005136,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266916	Chromatin interaction
ENSG00000188227	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1015848	0.89[EUR][1000 genomes]
rs1015849	0.93[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs1035479	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10403582	0.87[EUR][1000 genomes]
rs10404920	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs10404945	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes]
rs10405064	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs10405325	0.81[EUR][1000 genomes]
rs10405407	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs10406177	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10407084	0.93[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10409204	0.93[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs10411574	0.97[EUR][1000 genomes]
rs10413602	0.82[EUR][1000 genomes]
rs10414904	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs10415024	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs10415937	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs10417503	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs10417844	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs10420430	0.82[EUR][1000 genomes]
rs10420722	0.92[EUR][1000 genomes]
rs10420754	0.93[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10422074	0.82[EUR][1000 genomes]
rs10422667	0.89[EUR][1000 genomes]
rs10424574	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs10426618	0.89[EUR][1000 genomes]
rs11083426	0.92[EUR][1000 genomes]
rs11671972	0.80[ASN][1000 genomes]
rs12972252	0.89[EUR][1000 genomes]
rs12979470	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12981532	0.82[EUR][1000 genomes]
rs13343471	0.93[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs13343502	0.93[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs13345116	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs1373991	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs1382357	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1559229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1823061	0.81[CEU][hapmap];0.90[JPT][hapmap]
rs2045908	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2081096	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2112922	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2112923	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2126977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279148	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2279149	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2291004	1.00[CEU][hapmap];0.94[JPT][hapmap];0.96[EUR][1000 genomes]
rs2303131	0.93[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs28373708	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28538699	0.91[EUR][1000 genomes]
rs28605784	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28623164	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2891699	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35540940	0.96[EUR][1000 genomes]
rs35777021	0.87[EUR][1000 genomes]
rs3745765	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs3760825	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803895	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4417644	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs4452075	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4801759	0.93[CEU][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes]
rs4801803	0.93[CEU][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes]
rs4802766	0.93[EUR][1000 genomes]
rs4802889	0.96[EUR][1000 genomes]
rs4803195	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803210	0.88[CEU][hapmap]
rs4803229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4803460	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4803539	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59224125	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6508719	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6508732	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs713256	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs7246993	0.82[EUR][1000 genomes]
rs7247259	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs7248733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7252099	0.87[EUR][1000 genomes]
rs7252325	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7252346	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7253091	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255407	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7255785	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7255952	1.00[CEU][hapmap];0.88[JPT][hapmap];0.99[EUR][1000 genomes]
rs7255972	0.93[CEU][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs7255996	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7256130	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7257672	0.93[CEU][hapmap];0.86[JPT][hapmap]
rs7258692	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs73631095	0.91[EUR][1000 genomes]
rs7408563	0.93[CEU][hapmap];0.90[JPT][hapmap]
rs8106839	0.93[CEU][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes]
rs8109038	1.00[CEU][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes]
rs8109632	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8111782	0.93[CEU][hapmap];0.95[JPT][hapmap]
rs8112610	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304566	0.93[CEU][hapmap];0.94[JPT][hapmap]
rs9676739	0.91[EUR][1000 genomes]
rs9676967	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9917081	0.93[CEU][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers 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 target site	73 gene(s)	inside rSNPs	diseases
2	esv2757695	chr19:37794850-38051606	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv2758759	chr19:37794850-38051606	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv833819	chr19:37899501-38051599	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1056753	chr19:37963714-38015943	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37998400-38004800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:37998600-38001400	Weak transcription	Colonic Mucosa	Colon
3	chr19:37998600-38002400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:37998600-38002600	Weak transcription	Spleen	Spleen
5	chr19:37998600-38003200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr19:37998600-38003800	Weak transcription	Placenta	Placenta
7	chr19:37998600-38004200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:37998600-38004800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:37998600-38005200	Weak transcription	Psoas Muscle	Psoas
10	chr19:37998600-38008400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:37998800-38000600	Weak transcription	Fetal Stomach	stomach
12	chr19:37998800-38000800	Weak transcription	Fetal Intestine Large	intestine
13	chr19:37998800-38001200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:37998800-38002000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:37998800-38002000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr19:37998800-38002200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr19:37998800-38002200	Weak transcription	Aorta	Aorta
18	chr19:37998800-38002200	Weak transcription	Pancreas	Pancrea
19	chr19:37998800-38002400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr19:37998800-38002600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr19:37998800-38003800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr19:37998800-38006200	Weak transcription	Esophagus	oesophagus
23	chr19:37998800-38010800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:37998800-38014000	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr19:37998800-38021000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:37998800-38022600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:37999000-38000600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr19:37999000-38000600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:37999000-38001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:37999000-38001800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr19:37999000-38001800	Weak transcription	Fetal Muscle Leg	muscle
32	chr19:37999000-38002000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr19:37999000-38002000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:37999000-38002000	Weak transcription	Colon Smooth Muscle	Colon
35	chr19:37999000-38002000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr19:37999000-38002000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:37999000-38002200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr19:37999000-38002200	Weak transcription	Fetal Intestine Small	intestine
39	chr19:37999000-38002200	Weak transcription	Lung	lung
40	chr19:37999000-38002400	Weak transcription	Rectal Smooth Muscle	rectum
41	chr19:37999000-38003800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr19:37999000-38004000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:37999000-38004200	Weak transcription	Brain Substantia Nigra	brain
44	chr19:37999000-38006800	Weak transcription	NH-A	brain
45	chr19:37999000-38007000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:37999000-38010800	Weak transcription	Right Ventricle	heart
47	chr19:37999000-38011000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:37999000-38011400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:37999000-38013800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr19:37999000-38028800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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