Variant report

Variant	rs1877726
Chromosome Location	chr1:226077231-226077232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:226076704-226077684	HEK293-T-REx	kidney:	n/a	chr1:226076978-226076987

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:226061864..226068048-chr1:226072871..226078674,7	MCF-7	breast:
2	chr1:226068530..226073051-chr1:226075073..226079547,5	MCF-7	breast:

Variant related genes	Relation type
LEFTY1	TF binding region
ENSG00000196187	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs3753668	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs3766941	0.83[LWK][hapmap];0.89[YRI][hapmap]
rs3806257	0.88[YRI][hapmap]
rs3806259	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3820238	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4653437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][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	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv873231	chr1:226019653-226134471	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
7	nsv520628	chr1:226026406-226093362	Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	esv3335650	chr1:226074720-226125458	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	esv3369235	chr1:226075748-226127738	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1877726	NVL	cis	cerebellum	SCAN
rs1877726	PSEN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226071000-226078600	Weak transcription	Lung	lung
2	chr1:226071000-226083600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:226071200-226078200	Weak transcription	Gastric	stomach
4	chr1:226071200-226078200	Weak transcription	HMEC	breast
5	chr1:226071800-226078800	Weak transcription	Primary T cells from cord blood	blood
6	chr1:226072000-226081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr1:226072000-226081600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:226072000-226082000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:226073200-226079800	Enhancers	Liver	Liver
10	chr1:226074800-226078800	Enhancers	Fetal Stomach	stomach
11	chr1:226075400-226079200	Enhancers	Ovary	ovary
12	chr1:226075800-226077600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr1:226075800-226079000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:226076200-226078800	Enhancers	A549	lung
15	chr1:226076200-226079000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:226076400-226077400	Flanking Bivalent TSS/Enh	HepG2	liver
17	chr1:226076400-226078000	Enhancers	Fetal Kidney	kidney
18	chr1:226076400-226079000	Enhancers	Placenta	Placenta
19	chr1:226076600-226077600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr1:226076600-226077800	Weak transcription	Small Intestine	intestine
21	chr1:226076600-226078600	Enhancers	Fetal Muscle Leg	muscle
22	chr1:226076600-226079000	Enhancers	Fetal Intestine Small	intestine
23	chr1:226076600-226079800	Enhancers	Stomach Mucosa	stomach
24	chr1:226076600-226080400	Enhancers	Pancreas	Pancrea
25	chr1:226076800-226077400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:226076800-226077400	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:226076800-226077800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
28	chr1:226076800-226078600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:226076800-226079000	Enhancers	Fetal Lung	lung
30	chr1:226076800-226079600	Enhancers	Fetal Intestine Large	intestine
31	chr1:226076800-226079800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:226076800-226079800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr1:226076800-226079800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:226076800-226084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:226077000-226077400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr1:226077000-226077400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr1:226077000-226077600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr1:226077000-226077600	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:226077000-226077800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:226077000-226077800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
41	chr1:226077000-226078400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:226077000-226079200	Enhancers	H9 Cell Line	embryonic stem cell
43	chr1:226077000-226085200	Weak transcription	Spleen	Spleen
44	chr1:226077000-226099000	Weak transcription	Right Atrium	heart
45	chr1:226077200-226077400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
46	chr1:226077200-226077400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:226077200-226077400	Enhancers	Stomach Smooth Muscle	stomach
48	chr1:226077200-226077600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr1:226077200-226078800	Weak transcription	K562	blood
50	chr1:226077200-226079000	Enhancers	Colonic Mucosa	Colon

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