Variant report

Variant	rs3752844
Chromosome Location	chr5:1814369-1814370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1814005..1815834-chr5:1902994..1904612,2	MCF-7	breast:
2	chr5:1813864..1817727-chr5:1823867..1827166,3	MCF-7	breast:
3	chr5:1813480..1815357-chr5:1842711..1844470,2	K562	blood:
4	chr5:1800636..1804649-chr5:1810665..1816134,8	MCF-7	breast:
5	chr5:1806661..1808738-chr5:1813655..1815575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10074291	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10475109	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10866526	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11133910	0.82[YRI][hapmap]
rs11739312	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11740602	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11740753	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11741881	0.95[CEU][hapmap];0.93[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748427	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11750565	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1546252	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1546253	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17535295	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17535337	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17535721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1873926	0.83[YRI][hapmap]
rs2131588	0.95[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131589	0.95[CEU][hapmap];0.93[CHB][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2172530	0.86[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2353585	0.90[CEU][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3756343	0.83[YRI][hapmap]
rs3756344	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756345	0.83[YRI][hapmap]
rs3756346	0.83[YRI][hapmap]
rs3776141	0.83[YRI][hapmap]
rs3776142	0.83[YRI][hapmap]
rs3776149	0.83[YRI][hapmap]
rs3776152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3776154	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4147772	0.83[YRI][hapmap]
rs4147773	0.82[YRI][hapmap]
rs4147775	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4275010	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4277951	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4296838	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4296839	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4304110	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4416633	0.94[CEU][hapmap];0.92[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4588629	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4975848	0.83[YRI][hapmap]
rs4975849	0.83[YRI][hapmap]
rs4975852	0.85[YRI][hapmap]
rs4975853	0.83[YRI][hapmap]
rs60542979	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62338060	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62338061	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62338062	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6859338	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6862914	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6864281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6868515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6873986	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6880885	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6881253	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6890404	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6894566	0.95[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7701970	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7703762	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7714300	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs972890	0.83[YRI][hapmap]
rs972892	0.83[YRI][hapmap]

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	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv1033147	chr5:1717303-1815821	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
6	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
8	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv3386720	chr5:1814278-1814449	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3752844	MRPL36	cis	Muscle Skeletal	GTEx
rs3752844	MRPL36	cis	lymphoblastoid	seeQTL
rs3752844	MRPL36	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802600-1814400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr5:1802800-1816000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:1802800-1817800	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr5:1802800-1818400	Strong transcription	H1 Cell Line	embryonic stem cell
6	chr5:1802800-1818600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:1802800-1818800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr5:1802800-1821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:1802800-1821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:1802800-1822000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
14	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr5:1803000-1816200	Strong transcription	Lung	lung
19	chr5:1803000-1816800	Strong transcription	Fetal Intestine Large	intestine
20	chr5:1803000-1818200	Strong transcription	Fetal Muscle Leg	muscle
21	chr5:1803000-1818400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:1803000-1818400	Strong transcription	NHLF	lung
23	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:1803000-1822400	Strong transcription	A549	lung
25	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
26	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr5:1803000-1822800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:1803000-1822800	Strong transcription	Osteobl	bone
29	chr5:1803000-1823800	Strong transcription	Fetal Thymus	thymus
30	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:1803000-1825600	Strong transcription	Liver	Liver
33	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
36	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
39	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr5:1803200-1815400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr5:1803200-1819400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:1803200-1821800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:1803200-1822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:1803200-1823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
48	chr5:1803400-1818600	Strong transcription	Fetal Intestine Small	intestine
49	chr5:1803400-1821600	Strong transcription	Fetal Stomach	stomach
50	chr5:1803400-1822800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links