Variant report

Variant	rs4916389
Chromosome Location	chr1:171463431-171463432
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	chr1:171453426..171457241-chr1:171461305..171463614,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117523	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10753119	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753120	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10753121	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10753126	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10913176	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10913198	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs116358	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13722	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1626990	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1687057	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1687060	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1687061	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1687064	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs170969	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs182897	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1980512	0.84[YRI][hapmap];0.85[AFR][1000 genomes]
rs2015996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2038042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2179141	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2207193	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2223898	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2272809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2294289	0.94[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs235465	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs235466	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs235467	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs235469	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235470	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235473	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235476	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs235480	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235481	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235482	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235484	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235485	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs235487	0.85[ASN][1000 genomes]
rs235489	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235491	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235492	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235494	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235496	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs235497	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235500	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235503	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs235504	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235505	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235506	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs235508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235509	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235510	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235884	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235885	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs235887	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs235905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235908	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2421841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4276951	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4384265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916230	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916231	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916232	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4916391	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4916392	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4916393	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61814663	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61814673	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6697306	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6702990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7514441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7523355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7535195	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7536075	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536460	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7538827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7548158	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs760643	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs760644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs764206	0.83[CHB][hapmap]
rs954035	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][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	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv3512995	chr1:171329123-171994470	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	esv3512997	chr1:171329123-171994470	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv465639	chr1:171459507-171545051	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv548190	chr1:171459507-171545051	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4916389	DNM3OS	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171455800-171465400	Weak transcription	Lung	lung
2	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
3	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
4	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:171456400-171466000	Weak transcription	Fetal Intestine Small	intestine
7	chr1:171456400-171467200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr1:171456400-171467800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:171456400-171468400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:171456400-171470200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:171456400-171471200	Weak transcription	Thymus	Thymus
12	chr1:171456400-171473000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr1:171456400-171481800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:171456400-171483600	Weak transcription	Fetal Intestine Large	intestine
15	chr1:171456600-171467000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr1:171456600-171469600	Weak transcription	Fetal Stomach	stomach
17	chr1:171456800-171464200	Weak transcription	Fetal Brain Male	brain
18	chr1:171456800-171474800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:171457000-171464000	Weak transcription	Fetal Kidney	kidney
20	chr1:171457000-171465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:171457200-171469000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:171457600-171463600	Weak transcription	Brain Angular Gyrus	brain
23	chr1:171457600-171471000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:171457800-171463600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr1:171457800-171463800	Weak transcription	Aorta	Aorta
26	chr1:171457800-171463800	Weak transcription	Esophagus	oesophagus
27	chr1:171457800-171464600	Enhancers	Primary T cells from cord blood	blood
28	chr1:171457800-171482000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr1:171457800-171482200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr1:171458000-171463600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:171458000-171463800	Weak transcription	NH-A	brain
32	chr1:171458000-171463800	Weak transcription	Osteobl	bone
33	chr1:171458200-171471000	Weak transcription	Fetal Brain Female	brain
34	chr1:171458400-171463600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr1:171458600-171463600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:171459000-171482000	Weak transcription	HMEC	breast
37	chr1:171459800-171463800	Weak transcription	Fetal Heart	heart
38	chr1:171460400-171471800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:171460600-171465400	Weak transcription	Pancreas	Pancrea
40	chr1:171460600-171467200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:171460800-171463600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:171460800-171464400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:171460800-171464800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:171460800-171466000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:171460800-171467400	Weak transcription	HepG2	liver
46	chr1:171460800-171468000	Weak transcription	Dnd41	blood
47	chr1:171460800-171470200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:171460800-171470600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:171460800-171481400	Weak transcription	HSMM	muscle
50	chr1:171461000-171465200	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links