Variant report

Variant	rs883859
Chromosome Location	chr1:180940588-180940589
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	POLR2A	chr1:180940535-180940664	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:180940033-180940994	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180938068..180941019-chr1:181056460..181059037,4	K562	blood:
2	chr1:180932996..180935455-chr1:180937795..180941673,3	MCF-7	breast:
3	chr1:180940141..180942876-chr1:180990476..180992121,2	MCF-7	breast:
4	chr1:180933034..180938105-chr1:180938834..180942220,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234237	TF binding region
ENSG00000135823	Chromatin interaction
ENSG00000162783	Chromatin interaction
ENSG00000251520	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10494536	0.95[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10753232	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs10797662	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10797663	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12744212	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12752307	0.95[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap]
rs12754041	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1411478	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs1411479	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs2331903	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs3747957	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3789361	0.81[EUR][1000 genomes]
rs3789362	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs3789364	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs3827708	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4111520	0.89[JPT][hapmap]
rs4652547	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs4652548	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs6425658	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6425659	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6665134	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs71516924	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7528255	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528526	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs7546157	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7553330	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs7556005	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180905400-180940600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:180918600-180944800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:180922600-180949400	Strong transcription	Dnd41	blood
4	chr1:180923600-180944800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:180923600-180958800	Weak transcription	Small Intestine	intestine
6	chr1:180923800-180942800	Weak transcription	Fetal Lung	lung
7	chr1:180923800-180944800	Weak transcription	HUVEC	blood vessel
8	chr1:180923800-180944800	Weak transcription	NH-A	brain
9	chr1:180924000-180941600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr1:180924200-180941600	Weak transcription	Pancreas	Pancrea
11	chr1:180924200-180942000	Weak transcription	Liver	Liver
12	chr1:180924200-180943400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr1:180929000-180956200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:180930200-180950200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:180931600-180941800	Weak transcription	Placenta	Placenta
16	chr1:180931600-180950800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:180932000-180942600	Weak transcription	HSMMtube	muscle
18	chr1:180932000-180944800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:180932200-180941600	Weak transcription	Fetal Kidney	kidney
20	chr1:180932200-180942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:180932800-180943000	Strong transcription	Fetal Stomach	stomach
22	chr1:180933200-180947200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:180933400-180948000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:180933400-180974600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:180933600-180943400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:180933800-180944200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:180933800-180948800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:180934200-180943800	Strong transcription	Fetal Intestine Large	intestine
29	chr1:180935600-180940600	Genic enhancers	Fetal Muscle Leg	muscle
30	chr1:180936400-180941600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:180936600-180942400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:180936600-180944000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:180937200-180942400	Weak transcription	Fetal Heart	heart
34	chr1:180937600-180942200	Strong transcription	Fetal Intestine Small	intestine
35	chr1:180937600-180942400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:180937800-180943400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:180937800-180950200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:180937800-180950400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:180938000-180942200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:180938000-180942400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:180938000-180943200	Strong transcription	Spleen	Spleen
42	chr1:180938000-180943400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:180938000-180943400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:180938000-180944200	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr1:180938000-180947000	Strong transcription	Thymus	Thymus
46	chr1:180938200-180940800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:180938200-180941800	Strong transcription	NHEK	skin
48	chr1:180938200-180943600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:180938200-180946600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:180938400-180940600	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links