Variant report

Variant	rs474835
Chromosome Location	chr11:73956797-73956798
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:73692439..73694234-chr11:73954365..73957303,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175567	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10898954	0.96[CEU][hapmap];0.95[CHB][hapmap]
rs1614299	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1615115	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1726735	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1726744	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1726746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1726751	0.85[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1726752	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1783537	0.95[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1790381	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1790398	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1790399	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs1790404	0.89[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2848559	1.00[YRI][hapmap]
rs3018184	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4453265	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.89[TSI][hapmap]
rs474280	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs486577	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs490539	1.00[ASW][hapmap];0.83[CHD][hapmap];1.00[YRI][hapmap]
rs4944036	0.85[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap]
rs4944038	0.80[EUR][1000 genomes]
rs500608	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs556134	1.00[YRI][hapmap]
rs575096	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627354	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6592545	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap]
rs6592551	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs826033	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap]
rs826039	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs826056	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs826061	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs826062	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs826066	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs474835	P4HA3	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73885600-73957000	Weak transcription	Fetal Brain Male	brain
2	chr11:73907400-73969200	Weak transcription	HUVEC	blood vessel
3	chr11:73913800-73961800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:73915600-73960600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:73916000-73957000	Weak transcription	NHLF	lung
6	chr11:73921800-73957200	Weak transcription	Pancreas	Pancrea
7	chr11:73921800-73962000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr11:73924800-73959000	Weak transcription	Aorta	Aorta
9	chr11:73926400-73959000	Weak transcription	Esophagus	oesophagus
10	chr11:73926400-73961800	Weak transcription	Fetal Intestine Small	intestine
11	chr11:73936000-73968000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:73936200-73966600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr11:73936400-73967000	Strong transcription	HSMM	muscle
14	chr11:73936400-73967600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:73937400-73961800	Weak transcription	Spleen	Spleen
16	chr11:73938400-73957000	Weak transcription	Psoas Muscle	Psoas
17	chr11:73938800-73967400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr11:73941000-73967600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:73941000-73967800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:73942200-73962000	Weak transcription	Colonic Mucosa	Colon
21	chr11:73942400-73957400	Weak transcription	Small Intestine	intestine
22	chr11:73942600-73961600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:73942600-73962000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr11:73942800-73957400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr11:73942800-73961800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:73943000-73961400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:73943600-73956800	Weak transcription	NHEK	skin
28	chr11:73944000-73957000	Weak transcription	Fetal Stomach	stomach
29	chr11:73945200-73959200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:73945600-73966800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:73946600-73957200	Weak transcription	Gastric	stomach
32	chr11:73946600-73966600	Strong transcription	A549	lung
33	chr11:73947200-73957200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr11:73947600-73957000	Weak transcription	Thymus	Thymus
35	chr11:73947600-73957200	Weak transcription	Lung	lung
36	chr11:73947600-73961800	Weak transcription	Right Ventricle	heart
37	chr11:73949200-73957200	Weak transcription	Fetal Lung	lung
38	chr11:73949400-73964600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:73950000-73957000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr11:73950000-73963600	Weak transcription	Fetal Heart	heart
41	chr11:73950400-73956800	Weak transcription	Colon Smooth Muscle	Colon
42	chr11:73950400-73958000	Weak transcription	NHDF-Ad	bronchial
43	chr11:73950400-73966600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr11:73950600-73957200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr11:73951200-73957000	Weak transcription	Left Ventricle	heart
46	chr11:73951600-73957000	Weak transcription	Ovary	ovary
47	chr11:73951600-73957000	Weak transcription	GM12878-XiMat	blood
48	chr11:73951600-73957200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:73951600-73961600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr11:73951600-73961800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links