Variant report

Variant	rs7254214
Chromosome Location	chr19:42368738-42368739
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
2	chr1:207503537..207504067-chr19:42368282..42368782,2	Hela-S3	cervix:
3	chr19:42367000..42368909-chr19:42375795..42378988,3	MCF-7	breast:
4	chr19:42367135..42368961-chr19:42460272..42462681,2	K562	blood:
5	chr19:42343167..42345193-chr19:42366399..42369039,2	K562	blood:
6	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
7	chr19:42311416..42313552-chr19:42366859..42369350,2	MCF-7	breast:
8	chr19:42366833..42368938-chr19:42528843..42531497,3	K562	blood:
9	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:

No data

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

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10404939	1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs10405900	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10408367	0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap]
rs10414356	0.83[ASN][1000 genomes]
rs10414823	0.95[CHB][hapmap]
rs10415452	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10416824	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs10417985	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500284	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12461099	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461131	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976571	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12979253	0.95[CHB][hapmap];0.83[CHD][hapmap]
rs12984383	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366610	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];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428922	0.85[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1457144	0.82[ASW][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1870092	1.00[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap]
rs1870093	0.81[ASN][1000 genomes]
rs2008798	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs2075749	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075750	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075752	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075754	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[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];0.96[ASN][1000 genomes]
rs2199829	0.91[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2290695	0.91[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2305809	0.80[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3786536	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786538	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]
rs3810153	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3922888	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4130852	0.83[ASN][1000 genomes]
rs4803511	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs4803512	0.82[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs58857981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509001	0.84[ASN][1000 genomes]
rs6509002	0.80[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs7248641	0.82[ASN][1000 genomes]
rs7250787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7251336	0.82[CHB][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap]
rs7251960	0.82[CHB][hapmap]
rs7257666	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258163	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7259967	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs734107	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs73549152	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104958	0.82[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[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];0.82[JPT][hapmap]
rs8113780	0.82[ASN][1000 genomes]
rs873282	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]
rs882520	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs891167	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs899662	0.86[CHB][hapmap];0.82[JPT][hapmap];0.96[LWK][hapmap]
rs930102	0.93[AMR][1000 genomes];0.97[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7254214	PPP5C	cis	parietal	SCAN
rs7254214	SLC1A5	cis	parietal	SCAN
rs7254214	GLTSCR2	cis	cerebellum	SCAN
rs7254214	LIG1	cis	parietal	SCAN
rs7254214	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs7254214	ZNF575	cis	parietal	SCAN
rs7254214	EXOC3L2	cis	cerebellum	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	chr19:42365600-42368800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:42365600-42368800	Genic enhancers	Gastric	stomach
14	chr19:42365600-42368800	Genic enhancers	Lung	lung
15	chr19:42365600-42369600	Genic enhancers	Pancreas	Pancrea
16	chr19:42365600-42370000	Genic enhancers	Fetal Muscle Leg	muscle
17	chr19:42365600-42370800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:42365600-42374600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr19:42365600-42374800	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr19:42365800-42368800	Genic enhancers	Fetal Stomach	stomach
21	chr19:42365800-42368800	Genic enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:42365800-42368800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr19:42365800-42369000	Strong transcription	Pancreatic Islets	Pancreatic Islet
24	chr19:42365800-42369000	Genic enhancers	Rectal Mucosa Donor 29	rectum
25	chr19:42365800-42369200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr19:42365800-42369600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr19:42365800-42370800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr19:42365800-42374600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr19:42365800-42374800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
31	chr19:42366000-42369000	Genic enhancers	NHDF-Ad	bronchial
32	chr19:42366000-42369200	Genic enhancers	Stomach Smooth Muscle	stomach
33	chr19:42366000-42369600	Strong transcription	Fetal Kidney	kidney
34	chr19:42366000-42370800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr19:42366000-42374800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
37	chr19:42366200-42369000	Genic enhancers	H1 Cell Line	embryonic stem cell
38	chr19:42366200-42369000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr19:42366200-42369200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:42366200-42370400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:42366200-42371000	Genic enhancers	Colonic Mucosa	Colon
42	chr19:42366400-42369600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr19:42366400-42369800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
44	chr19:42366400-42369800	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
46	chr19:42366600-42369400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:42366600-42374400	Strong transcription	Thymus	Thymus
48	chr19:42366600-42375000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:42366800-42369200	Genic enhancers	NH-A	brain
50	chr19:42366800-42370000	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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