Variant report

Variant	rs3108598
Chromosome Location	chr19:37068235-37068236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37063014..37065659-chr19:37066533..37068326,2	MCF-7	breast:
2	chr19:37062757..37067111-chr19:37067178..37071986,8	K562	blood:
3	chr19:37017864..37019585-chr19:37067468..37069306,2	K562	blood:
4	chr19:37062757..37066475-chr19:37067178..37075829,11	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092295.7.1-3	chr19:37068043-37068817	ENSG00000233527.4

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000186020	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10402486	0.85[ASN][1000 genomes]
rs11670917	0.80[ASN][1000 genomes]
rs17206393	0.86[CEU][hapmap];0.91[GIH][hapmap]
rs1830031	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap]
rs2033077	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs2245366	0.86[CEU][hapmap];0.86[GIH][hapmap]
rs2385642	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2385643	0.96[ASN][1000 genomes]
rs2385797	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs2912415	0.86[CEU][hapmap]
rs2912441	0.86[CEU][hapmap];0.91[GIH][hapmap]
rs2967453	0.87[ASN][1000 genomes]
rs2967539	0.86[CEU][hapmap];0.93[GIH][hapmap]
rs2967540	0.86[CEU][hapmap];0.93[GIH][hapmap]
rs3096617	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[ASN][1000 genomes]
rs3096618	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[ASN][1000 genomes]
rs3096619	0.91[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs3096622	0.96[ASN][1000 genomes]
rs3096623	0.96[ASN][1000 genomes]
rs3096627	0.96[ASN][1000 genomes]
rs3096628	0.96[ASN][1000 genomes]
rs3096629	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096630	0.94[ASN][1000 genomes]
rs3096631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs3096632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs3096633	0.83[ASN][1000 genomes]
rs3096636	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs3108166	0.85[ASN][1000 genomes]
rs3108167	0.87[ASN][1000 genomes]
rs3108168	0.88[ASN][1000 genomes]
rs3108171	0.94[CHB][hapmap]
rs3108172	0.83[ASN][1000 genomes]
rs3108174	0.87[ASN][1000 genomes]
rs3108181	0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3108184	0.80[ASN][1000 genomes]
rs3108185	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3108186	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3108187	0.80[ASN][1000 genomes]
rs3108188	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3108189	0.80[ASN][1000 genomes]
rs3108191	0.94[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs3108193	0.85[ASN][1000 genomes]
rs3108196	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108201	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3108203	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108205	0.82[ASN][1000 genomes]
rs3108208	0.85[ASN][1000 genomes]
rs3108209	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108214	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap]
rs3108215	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs3108543	0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3108544	0.83[ASN][1000 genomes]
rs3108545	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108546	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs3108549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs3108552	0.85[ASN][1000 genomes]
rs3108555	0.82[ASN][1000 genomes]
rs3108559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3108560	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs3108562	0.80[ASN][1000 genomes]
rs3108564	0.80[ASN][1000 genomes]
rs3108567	0.99[ASN][1000 genomes]
rs3108580	0.93[CHD][hapmap];0.99[ASN][1000 genomes]
rs3108594	0.99[ASN][1000 genomes]
rs3108596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs3108597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3108600	0.96[ASN][1000 genomes]
rs3108602	0.96[ASN][1000 genomes]
rs3108603	0.96[ASN][1000 genomes]
rs3108604	0.83[ASN][1000 genomes]
rs3108607	0.87[ASN][1000 genomes]
rs3108608	0.85[ASN][1000 genomes]
rs3108609	0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs3108610	0.85[ASN][1000 genomes]
rs3111541	0.99[ASN][1000 genomes]
rs3111542	0.99[ASN][1000 genomes]
rs3111547	0.96[ASN][1000 genomes]
rs3111549	0.86[ASN][1000 genomes]
rs3111550	0.83[ASN][1000 genomes]
rs34002069	0.85[ASN][1000 genomes]
rs34395293	0.96[ASN][1000 genomes]
rs34550124	0.80[ASN][1000 genomes]
rs4806336	0.96[ASN][1000 genomes]
rs4806351	0.87[CEU][hapmap]
rs62113945	0.87[ASN][1000 genomes]
rs7245414	0.85[ASN][1000 genomes]
rs7248477	0.87[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7259256	0.94[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]

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	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers 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	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	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
7	esv3334779	chr19:37050161-37076919	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3108598	PPP1R14A	cis	cerebellum	SCAN
rs3108598	LGALS4	cis	parietal	SCAN
rs3108598	PSG4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37064600-37068800	ZNF genes & repeats	A549	lung
2	chr19:37065600-37068600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:37065600-37069600	Weak transcription	Psoas Muscle	Psoas
4	chr19:37065600-37070200	Weak transcription	HSMMtube	muscle
5	chr19:37065600-37070200	Weak transcription	NHLF	lung
6	chr19:37065600-37081200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:37065600-37095400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr19:37065800-37068400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:37065800-37068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:37065800-37068400	Weak transcription	Right Atrium	heart
11	chr19:37065800-37069400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr19:37065800-37070000	Weak transcription	Brain Angular Gyrus	brain
13	chr19:37065800-37071200	Weak transcription	Brain Substantia Nigra	brain
14	chr19:37065800-37072000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:37065800-37072600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr19:37065800-37075200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr19:37065800-37076600	Weak transcription	Stomach Mucosa	stomach
18	chr19:37065800-37078200	Weak transcription	Right Ventricle	heart
19	chr19:37066000-37070200	Weak transcription	Brain Anterior Caudate	brain
20	chr19:37066000-37081200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:37066000-37081200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37066200-37070200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:37066200-37070200	Weak transcription	Fetal Brain Male	brain
24	chr19:37066200-37070200	Weak transcription	Fetal Heart	heart
25	chr19:37066200-37071400	Weak transcription	HepG2	liver
26	chr19:37066200-37073200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:37066600-37070200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
28	chr19:37066600-37072000	Strong transcription	HUVEC	blood vessel
29	chr19:37066600-37073200	Strong transcription	Fetal Muscle Leg	muscle
30	chr19:37066600-37073400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr19:37066600-37073400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:37066600-37073400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
33	chr19:37066600-37074200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:37066600-37074200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr19:37066600-37080600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr19:37066800-37070200	ZNF genes & repeats	Fetal Intestine Large	intestine
37	chr19:37066800-37070200	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr19:37066800-37070600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:37066800-37074400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:37066800-37081000	Strong transcription	Dnd41	blood
41	chr19:37066800-37091400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr19:37067000-37069800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr19:37067000-37070200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr19:37067000-37072200	Strong transcription	Stomach Smooth Muscle	stomach
45	chr19:37067000-37073200	Strong transcription	Placenta	Placenta
46	chr19:37067000-37073800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:37067000-37076200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:37067000-37076800	ZNF genes & repeats	GM12878-XiMat	blood
49	chr19:37067000-37080800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:37067000-37081200	ZNF genes & repeats	Liver	Liver

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