Variant report

Variant	rs604495
Chromosome Location	chr19:23581887-23581888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF91-1	chr19:23581791-23583851	NONHSAT063906

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10415339	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10417541	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1044095	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10854068	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11879939	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1821845	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2127370	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885846	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293895	0.90[ASN][1000 genomes]
rs295413	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs295418	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29983	0.87[ASN][1000 genomes]
rs29984	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29985	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29986	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs29988	0.89[CEU][hapmap];0.87[ASN][1000 genomes]
rs29989	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29990	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36119092	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40561	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs423265	0.93[ASN][1000 genomes]
rs429771	0.90[ASN][1000 genomes]
rs431270	0.92[CHB][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.90[ASN][1000 genomes]
rs61738904	0.83[ASN][1000 genomes]
rs6511434	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs771701	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription 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	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
12	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
13	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	esv3332495	chr19:23451842-23598069	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
15	esv3319024	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
16	esv3319025	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
17	esv3447830	chr19:23465035-23610690	Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
18	esv3382338	chr19:23476728-23631356	Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
19	esv3323302	chr19:23477342-23648545	ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
20	esv3523857	chr19:23477614-23632199	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
21	esv3523858	chr19:23477614-23632199	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
22	esv3334120	chr19:23545829-23837686	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
23	nsv960817	chr19:23556437-23606658	ZNF genes & repeats Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
24	nsv1064929	chr19:23559483-23827735	Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
25	nsv1057474	chr19:23563612-23812441	ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
26	nsv543962	chr19:23563612-23812441	ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs604495	ZNF85	cis	parietal	SCAN
rs604495	ZNF91	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23578200-23598000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:23578400-23582000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:23578400-23582200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:23578400-23582200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:23578400-23585000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:23578400-23585200	Weak transcription	Esophagus	oesophagus
7	chr19:23578400-23586800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:23578400-23592200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:23578400-23597600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:23578600-23582400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr19:23578600-23583000	Weak transcription	Fetal Lung	lung
12	chr19:23578600-23597800	Weak transcription	Fetal Stomach	stomach
13	chr19:23578800-23582000	Weak transcription	Fetal Intestine Large	intestine
14	chr19:23578800-23582200	Weak transcription	HepG2	liver
15	chr19:23578800-23583200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:23578800-23583200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:23579000-23582000	Weak transcription	Brain Germinal Matrix	brain
18	chr19:23579000-23582200	Weak transcription	Fetal Intestine Small	intestine
19	chr19:23579000-23583200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr19:23580600-23582400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr19:23581200-23586800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr19:23581200-23590600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:23581400-23582400	Weak transcription	Placenta	Placenta
24	chr19:23581400-23589000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:23581400-23590600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:23581600-23585400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
27	chr19:23581600-23586000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:23581600-23590200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:23581600-23591000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:23581600-23591200	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:23581600-23591200	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:23581800-23582600	Strong transcription	Fetal Brain Female	brain
33	chr19:23581800-23584000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr19:23581800-23588400	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr19:23581800-23591000	Strong transcription	HUES48 Cell Line	embryonic stem cell

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