Variant report

Variant	rs13105060
Chromosome Location	chr4:151505322-151505323
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:151504945-151505507	SK-N-SH	brain:	n/a	n/a
2	MAX	chr4:151503931-151505387	SK-N-SH	brain:	n/a	n/a
3	MXI1	chr4:151502161-151505676	IMR90	lung:	n/a	n/a
4	SUZ12	chr4:151503416-151505330	NT2-D1	testis:	n/a	n/a
5	SIN3AK20	chr4:151504727-151505371	SK-N-SH	brain:	n/a	n/a
6	TAF1	chr4:151504961-151505351	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr4:151505066-151505351	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr4:151502343-151506138	H1-neurons	neurons:	n/a	n/a
9	TCF12	chr4:151505111-151505374	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr4:151503901-151505368	IMR90	lung:	n/a	n/a
11	POLR2A	chr4:151499806-151506108	H1-neurons	neurons:	n/a	n/a
12	MXI1	chr4:151502292-151505889	SK-N-SH	brain:	n/a	n/a
13	SIN3A	chr4:151502749-151505409	H1-hESC	embryonic stem cell:	n/a	n/a
14	NFIC	chr4:151504438-151505572	SK-N-SH	brain:	n/a	n/a
15	MAX	chr4:151504311-151505391	SK-N-SH	brain:	n/a	n/a
16	CTBP2	chr4:151503424-151505364	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:151505300..151507598-chr4:151514768..151516765,2	K562	blood:
2	chr4:151494137..151496884-chr4:151503865..151506422,4	K562	blood:
3	chr4:151495333..151496884-chr4:151503356..151505383,3	K562	blood:

No data

Variant related genes	Relation type
LRBA	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10003085	0.86[JPT][hapmap]
rs10008675	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10010950	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10011917	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10027710	0.86[JPT][hapmap]
rs10520078	0.87[JPT][hapmap]
rs11099769	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11099770	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11099772	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12499524	0.86[EUR][1000 genomes]
rs12503291	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12505967	0.87[JPT][hapmap]
rs12510904	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13108157	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13145482	0.87[JPT][hapmap]
rs13147825	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4309819	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4318628	0.87[JPT][hapmap]
rs4336204	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4336207	0.87[JPT][hapmap]
rs4435730	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577554	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4585281	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4642231	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4696463	0.86[EUR][1000 genomes]
rs6826066	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6835367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6858706	0.92[JPT][hapmap]
rs7657997	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868664	0.86[EUR][1000 genomes]
rs9884181	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880256	chr4:151126725-151751369	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv817540	chr4:151228965-151858609	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv869051	chr4:151347901-151737781	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1024820	chr4:151364078-151943561	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1018942	chr4:151423295-151556444	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv537301	chr4:151423295-151556444	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv4547	chr4:151486280-151531479	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:151486600-151510400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:151487200-151655000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr4:151497600-151535400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:151499000-151513000	Active TSS	Colon Smooth Muscle	Colon
5	chr4:151499000-151513200	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr4:151499800-151506000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr4:151500000-151543400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:151500800-151505400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:151500800-151505600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr4:151500800-151511800	Active TSS	Osteobl	bone
11	chr4:151500800-151520000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr4:151501200-151506400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr4:151501200-151559800	Weak transcription	Ovary	ovary
14	chr4:151501400-151506000	Strong transcription	Primary T cells from cord blood	blood
15	chr4:151501400-151514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:151501800-151512400	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr4:151502200-151507800	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr4:151502400-151505600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr4:151502400-151506000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr4:151502600-151505600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
21	chr4:151502600-151505600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr4:151502600-151505600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
23	chr4:151502600-151507600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:151502800-151505400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:151502800-151505400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
26	chr4:151502800-151505400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
27	chr4:151502800-151505400	Active TSS	Right Ventricle	heart
28	chr4:151502800-151505800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr4:151503000-151505400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:151503000-151505600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr4:151503000-151506000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
32	chr4:151503200-151505400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:151503200-151505400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:151503400-151505400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr4:151503400-151505400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr4:151503400-151505400	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr4:151503400-151505400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
38	chr4:151503400-151505400	ZNF genes & repeats	Thymus	Thymus
39	chr4:151503400-151506000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr4:151503400-151507000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:151503600-151505400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr4:151503600-151505600	ZNF genes & repeats	Fetal Thymus	thymus
43	chr4:151503600-151505800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr4:151503600-151506000	ZNF genes & repeats	GM12878-XiMat	blood
45	chr4:151503800-151505600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr4:151503800-151505600	Active TSS	Brain Hippocampus Middle	brain
47	chr4:151503800-151505600	Active TSS	Small Intestine	intestine
48	chr4:151504000-151505400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:151504000-151505400	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr4:151504000-151505400	ZNF genes & repeats	Pancreas	Pancrea

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