Variant report

Variant	rs13114343
Chromosome Location	chr4:103189416-103189417
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	chr4:102265718..102267485-chr4:103187307..103189886,2	MCF-7	breast:

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs11736058	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13111744	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13111958	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13111982	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13112133	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13126885	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs149268	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151370	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs151402	0.82[JPT][hapmap]
rs151413	0.86[ASN][1000 genomes]
rs151414	0.88[ASN][1000 genomes]
rs151416	0.86[ASN][1000 genomes]
rs151417	0.82[ASN][1000 genomes]
rs182865	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs190178	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs192068	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119213	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2165265	0.91[CHB][hapmap]
rs233818	0.88[CHB][hapmap]
rs34376460	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34922141	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35301460	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35610681	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35700174	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs366374	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs368845	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs373091	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs380768	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs384085	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs384460	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs386682	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs387839	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs394649	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs406749	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs406954	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs408364	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs412428	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs413462	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs418348	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs420823	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430589	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431984	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs432186	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs438803	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs440507	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs444943	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4476601	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs448181	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs451078	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs452385	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4525979	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455610	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs455741	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs456349	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs456521	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs456985	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs457490	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs457736	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs458201	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs458943	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459159	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459331	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs459559	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs460026	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs460610	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs460755	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs461902	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4621433	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs462186	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs463542	0.85[ASN][1000 genomes]
rs463721	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs463772	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4640675	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465144	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs465176	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs467204	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs593576	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62327916	0.80[ASN][1000 genomes]
rs642663	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs643119	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs643645	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs657195	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs658953	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs659837	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs660502	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs660580	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs682916	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs688499	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9995079	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869164	chr4:102483189-103213842	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv428447	chr4:103103730-103262107	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1008680	chr4:103153709-103206555	Strong transcription Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1011868	chr4:103158581-103206555	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv999012	chr4:103162076-103206555	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1012254	chr4:103174196-103191787	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1014733	chr4:103174196-103206240	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1002129	chr4:103174196-103206555	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1013313	chr4:103175700-103206555	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1013439	chr4:103178743-103191787	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1003825	chr4:103179197-103206555	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv998689	chr4:103179788-103206555	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13114343	SLC39A8	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103179200-103202200	Weak transcription	Lung	lung
2	chr4:103179400-103221000	Weak transcription	K562	blood
3	chr4:103180400-103200400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:103181400-103197600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:103181600-103210800	Weak transcription	Liver	Liver
6	chr4:103181800-103230400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:103182000-103255400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr4:103183400-103210600	Weak transcription	Primary B cells from cord blood	blood
9	chr4:103184000-103196600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:103184200-103220600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr4:103184400-103190200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr4:103184600-103200400	Weak transcription	GM12878-XiMat	blood
13	chr4:103184600-103201000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:103186600-103195400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr4:103186600-103229600	Weak transcription	Pancreas	Pancrea
16	chr4:103186800-103216800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:103187200-103200400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:103187200-103229400	Weak transcription	Fetal Thymus	thymus
19	chr4:103187600-103189600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr4:103188400-103192600	Weak transcription	Hela-S3	cervix
21	chr4:103188400-103194000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:103188600-103189800	Strong transcription	Dnd41	blood
23	chr4:103189000-103189800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:103189000-103193000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:103189000-103216800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:103189200-103192200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr4:103189200-103192600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:103189200-103195800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr4:103189200-103197600	Weak transcription	Primary T cells from cord blood	blood
30	chr4:103189200-103211200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr4:103189200-103225400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr4:103189400-103218600	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links