Variant report

Variant	rs873282
Chromosome Location	chr19:42367906-42367907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42346899..42349395-chr19:42366337..42367958,2	K562	blood:
2	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
3	chr19:42366555..42368141-chr19:42405130..42408050,2	K562	blood:
4	chr19:42367000..42368909-chr19:42375795..42378988,3	MCF-7	breast:
5	chr19:42367135..42368961-chr19:42460272..42462681,2	K562	blood:
6	chr19:42343167..42345193-chr19:42366399..42369039,2	K562	blood:
7	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
8	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
9	chr19:42366833..42368695-chr19:42529044..42531497,2	K562	blood:
10	chr19:42311416..42313552-chr19:42366859..42369350,2	MCF-7	breast:
11	chr19:42366833..42368938-chr19:42528843..42531497,3	K562	blood:
12	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
13	chr19:42361079..42367934-chr19:42431466..42436133,8	K562	blood:
14	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183103	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000170956	Chromatin interaction
ENSG00000142025	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10404939	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs10405900	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs10414356	0.84[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs10415452	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];0.89[YRI][hapmap]
rs10417985	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs12461099	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12976571	1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12979253	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs12984383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1366610	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1428922	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1457144	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1870092	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs1870093	0.82[ASN][1000 genomes]
rs2008798	0.90[CHB][hapmap];0.83[JPT][hapmap];0.94[YRI][hapmap]
rs2075749	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075750	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075752	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2075754	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2290695	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[ASN][1000 genomes]
rs2305809	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs28824227	0.82[AFR][1000 genomes]
rs3786536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs3810153	0.85[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs3922888	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4130852	0.84[ASN][1000 genomes]
rs4803511	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs4803512	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs58857981	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508999	0.82[AFR][1000 genomes]
rs6509001	0.85[ASN][1000 genomes]
rs6509002	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap]
rs7248641	0.82[ASN][1000 genomes]
rs7250787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7254214	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257666	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258163	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259596	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259967	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs734107	0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.89[YRI][hapmap]
rs73549152	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8104958	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs8106505	0.95[CHB][hapmap]
rs8113283	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs8113641	0.89[CHB][hapmap];0.83[JPT][hapmap]
rs8113780	0.82[ASN][1000 genomes]
rs882520	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs891167	0.81[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs899662	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs930102	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats 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
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs873282	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs873282	RPS19	cis	Esophagus Muscularis	GTEx
rs873282	GLTSCR2	cis	cerebellum	SCAN
rs873282	EXOC3L2	cis	cerebellum	SCAN
rs873282	SLC1A5	cis	parietal	SCAN
rs873282	LIG1	cis	parietal	SCAN
rs873282	ZNF575	cis	parietal	SCAN
rs873282	PPP5C	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42364600-42368800	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:42364600-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:42364800-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr19:42365200-42368800	Genic enhancers	Spleen	Spleen
5	chr19:42365200-42369600	Transcr. at gene 5' and 3'	Hela-S3	cervix
6	chr19:42365400-42369200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
7	chr19:42365400-42369800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
8	chr19:42365400-42374800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr19:42365400-42375000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr19:42365600-42368000	Genic enhancers	Placenta	Placenta
13	chr19:42365600-42368400	Genic enhancers	Brain Cingulate Gyrus	brain
14	chr19:42365600-42368400	Genic enhancers	Stomach Mucosa	stomach
15	chr19:42365600-42368800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:42365600-42368800	Genic enhancers	Gastric	stomach
17	chr19:42365600-42368800	Genic enhancers	Lung	lung
18	chr19:42365600-42369600	Genic enhancers	Pancreas	Pancrea
19	chr19:42365600-42370000	Genic enhancers	Fetal Muscle Leg	muscle
20	chr19:42365600-42370800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr19:42365600-42374600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr19:42365600-42374800	Genic enhancers	Primary T cells fromperipheralblood	blood
23	chr19:42365800-42368800	Genic enhancers	Fetal Stomach	stomach
24	chr19:42365800-42368800	Genic enhancers	Rectal Mucosa Donor 31	rectum
25	chr19:42365800-42368800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
26	chr19:42365800-42369000	Strong transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:42365800-42369000	Genic enhancers	Rectal Mucosa Donor 29	rectum
28	chr19:42365800-42369200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:42365800-42369600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:42365800-42370800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr19:42365800-42374600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr19:42365800-42374800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
34	chr19:42366000-42369000	Genic enhancers	NHDF-Ad	bronchial
35	chr19:42366000-42369200	Genic enhancers	Stomach Smooth Muscle	stomach
36	chr19:42366000-42369600	Strong transcription	Fetal Kidney	kidney
37	chr19:42366000-42370800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr19:42366000-42374800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
39	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
40	chr19:42366200-42368600	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:42366200-42369000	Genic enhancers	H1 Cell Line	embryonic stem cell
42	chr19:42366200-42369000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr19:42366200-42369200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:42366200-42370400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:42366200-42371000	Genic enhancers	Colonic Mucosa	Colon
46	chr19:42366400-42369600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr19:42366400-42369800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
48	chr19:42366400-42369800	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
50	chr19:42366600-42368400	Weak transcription	Psoas Muscle	Psoas

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