Variant report

Variant	rs401824
Chromosome Location	chr19:36342909-36342910
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36342859-36342909	PFSK-1	brain:	n/a
2	chr19:36342859-36342909	HIPEpiC	eye:	n/a
3	chr19:36342859-36342909	ovcar-3	ovarian:	n/a
4	chr19:36342859-36342909	HUVEC	blood vessel:	n/a
5	chr19:36342859-36342909	AG04450	lung:	fetal
6	chr19:36342859-36342909	GM12891	blood:	n/a
7	chr19:36342859-36342909	Hela-S3	cervix:	n/a
8	chr19:36342859-36342909	Hepatocyte	liver:	n/a
9	chr19:36342859-36342909	SKMC	muscle:	n/a
10	chr19:36342859-36342909	AG04449	skin:	fetal
11	chr19:36342859-36342909	HMEC	breast:	n/a
12	chr19:36342859-36342909	CMK	blood:	n/a
13	chr19:36342859-36342909	SK-N-MC	brain:	n/a
14	chr19:36342859-36342909	HRCEpiC	kidney:	n/a
15	chr19:36342859-36342909	HRE	kidney:	n/a
16	chr19:36342859-36342909	HCPEpiC	choroid plexus:	n/a
17	chr19:36342859-36342909	GM12878	blood:	n/a
18	chr19:36342859-36342909	HRPEpiC	eye:	n/a
19	chr19:36342859-36342909	HCT-116	colon:	n/a
20	chr19:36342859-36342909	BE2_C	brain:	n/a
21	chr19:36342859-36342909	U87	brain:	n/a
22	chr19:36342859-36342909	MCF10A-Er-Src	breast:	n/a
23	chr19:36342859-36342909	AoSMC	blood vessel:	n/a
24	chr19:36342859-36342909	IMR90	lung:	fetal
25	chr19:36342859-36342909	GM12892	blood:	n/a
26	chr19:36342859-36342909	PrEC	prostate:	n/a
27	chr19:36342859-36342909	SK-N-SH	brain:	n/a
28	chr19:36342859-36342909	HEK293	kidney:	embryo
29	chr19:36342859-36342909	A549	lung:	n/a
30	chr19:36342859-36342909	NHBE	bronchial:	n/a
31	chr19:36342859-36342909	Caco-2	colon:	n/a
32	chr19:36342859-36342909	HepG2	liver:	n/a
33	chr19:36342859-36342909	Jurkat	blood:	n/a
34	chr19:36342859-36342909	HNPCEpiC	eye:	n/a
35	chr19:36342859-36342909	T-47D	breast:	n/a
36	chr19:36342859-36342909	NH-A	brain:	n/a
37	chr19:36342859-36342909	ECC-1	luminal epithelium:	n/a
38	chr19:36342859-36342909	LNCaP	prostate:	n/a
39	chr19:36342859-36342909	NB4	blood:	n/a
40	chr19:36342859-36342909	HCF	heart:	n/a
41	chr19:36342859-36342909	HCM	heart:	n/a
42	chr19:36342859-36342909	HEEpiC	esophagus:	n/a
43	chr19:36342859-36342909	MCF-7	breast:	n/a
44	chr19:36342859-36342909	RPTEC	kidney:	n/a
45	chr19:36342859-36342909	HPAEpiC	pulmonary alveolar:	n/a
46	chr19:36342859-36342909	HAEpiC	amniotic membrane:	n/a
47	chr19:36342859-36342909	ProgFib	skin:	n/a
48	chr19:36342859-36342909	PANC-1	pancreas:	n/a
49	chr19:36342859-36342909	SK-N-SH_RA	brain:	n/a
50	chr19:36342859-36342909	AG09319	gingival:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36341339..36343391-chr19:36346097..36348874,2	MCF-7	breast:
2	chr19:36336403..36338756-chr19:36340642..36343905,3	MCF-7	breast:

No data

Variant related genes	Relation type
NPHS1	CpG island
KIRREL2	CpG island
ENSG00000161270	Chromatin interaction
ENSG00000126259	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11084834	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11880909	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11881358	0.95[EUR][1000 genomes]
rs11881364	0.95[EUR][1000 genomes]
rs11881451	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16970735	0.95[EUR][1000 genomes]
rs16970737	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16970742	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs16970744	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs172985	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2227909	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2285450	0.92[JPT][hapmap]
rs230260	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs230261	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs230262	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs230263	0.95[EUR][1000 genomes]
rs230264	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs230265	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs230266	0.95[EUR][1000 genomes]
rs230267	0.95[EUR][1000 genomes]
rs230268	0.86[EUR][1000 genomes]
rs230269	0.95[EUR][1000 genomes]
rs2871778	1.00[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs34006827	0.95[EUR][1000 genomes]
rs35423326	0.95[EUR][1000 genomes]
rs376240	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs392702	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs393116	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs404299	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs412175	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs417786	0.81[EUR][1000 genomes]
rs437168	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.85[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs443186	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs447783	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55797913	0.95[EUR][1000 genomes]
rs55816190	0.95[EUR][1000 genomes]
rs56264349	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57053076	0.95[EUR][1000 genomes]
rs57668132	0.95[EUR][1000 genomes]
rs58098901	0.95[EUR][1000 genomes]
rs58109577	0.95[EUR][1000 genomes]
rs58291714	0.89[EUR][1000 genomes]
rs59123406	0.95[EUR][1000 genomes]
rs59658571	0.95[EUR][1000 genomes]
rs60268250	0.89[EUR][1000 genomes]
rs60576074	0.89[EUR][1000 genomes]
rs60869994	0.89[EUR][1000 genomes]
rs61623584	0.95[EUR][1000 genomes]
rs619833	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7248157	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs7251744	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7251879	1.00[MEX][hapmap];0.85[TSI][hapmap]
rs7258909	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73594463	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73928331	0.95[EUR][1000 genomes]
rs73928332	0.95[EUR][1000 genomes]
rs73928333	0.95[EUR][1000 genomes]
rs807660	0.95[EUR][1000 genomes]
rs8106732	0.95[EUR][1000 genomes]
rs8110926	0.95[EUR][1000 genomes]
rs8111209	0.95[EUR][1000 genomes]
rs8111348	0.95[EUR][1000 genomes]
rs8113704	1.00[MEX][hapmap]
rs879407	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9749325	0.95[EUR][1000 genomes]
rs9749492	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
5	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	esv3397651	chr19:36326933-36377725	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv833812	chr19:36331913-36507594	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
8	nsv833813	chr19:36341181-36499431	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv911639	chr19:36342909-36365985	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36337000-36347000	Weak transcription	Right Atrium	heart
2	chr19:36342000-36343800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr19:36342000-36344200	Active TSS	Pancreas	Pancrea
4	chr19:36342200-36343400	Active TSS	Fetal Kidney	kidney
5	chr19:36342200-36345600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:36342400-36343400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr19:36342600-36343000	Bivalent/Poised TSS	Fetal Intestine Small	intestine
8	chr19:36342600-36343400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr19:36342800-36343600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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