Variant report

Variant	rs852438
Chromosome Location	chr7:5661411-5661412
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:5661377..5664356-chr7:5673284..5675740,2	MCF-7	breast:
2	chr7:5650427..5652222-chr7:5660370..5662038,2	MCF-7	breast:

Extended variants
information (count: 132 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10271741	0.81[ASN][1000 genomes]
rs10807950	0.94[ASN][1000 genomes]
rs10951961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11763027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1640231	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1640234	1.00[JPT][hapmap]
rs1725186	1.00[ASN][1000 genomes]
rs1725187	1.00[ASN][1000 genomes]
rs1990835	0.94[ASN][1000 genomes]
rs2008418	0.81[ASN][1000 genomes]
rs2008425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2112008	0.94[ASN][1000 genomes]
rs2161012	0.94[ASN][1000 genomes]
rs2345863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2345864	0.94[ASN][1000 genomes]
rs2881234	0.82[ASN][1000 genomes]
rs28874635	0.81[ASN][1000 genomes]
rs2908430	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3735288	1.00[ASN][1000 genomes]
rs3857756	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4720636	0.94[ASN][1000 genomes]
rs4720639	0.94[ASN][1000 genomes]
rs4720643	1.00[CHB][hapmap]
rs4720645	0.81[ASN][1000 genomes]
rs4724714	0.94[ASN][1000 genomes]
rs4724716	0.94[ASN][1000 genomes]
rs4724720	0.94[ASN][1000 genomes]
rs4724721	0.94[ASN][1000 genomes]
rs4724723	0.94[ASN][1000 genomes]
rs4724727	0.81[ASN][1000 genomes]
rs4724732	0.81[ASN][1000 genomes]
rs4724734	0.81[ASN][1000 genomes]
rs62455878	0.81[ASN][1000 genomes]
rs6463508	0.94[ASN][1000 genomes]
rs6463515	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs66467570	0.81[ASN][1000 genomes]
rs6944453	0.81[ASN][1000 genomes]
rs6945676	0.81[ASN][1000 genomes]
rs6947405	0.94[ASN][1000 genomes]
rs6956990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6969486	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs710939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs710940	1.00[ASN][1000 genomes]
rs710942	1.00[ASN][1000 genomes]
rs7784394	0.94[ASN][1000 genomes]
rs7790499	0.94[ASN][1000 genomes]
rs7794571	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7803040	1.00[JPT][hapmap]
rs7809914	0.81[ASN][1000 genomes]
rs852261	0.94[ASN][1000 genomes]
rs852262	0.94[ASN][1000 genomes]
rs852264	0.94[ASN][1000 genomes]
rs852376	0.86[YRI][hapmap]
rs852378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852393	0.94[ASN][1000 genomes]
rs852395	0.94[ASN][1000 genomes]
rs852396	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs852397	0.83[YRI][hapmap]
rs852398	0.94[ASN][1000 genomes]
rs852399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs852401	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs852402	0.86[YRI][hapmap]
rs852403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs852404	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs852405	0.94[ASN][1000 genomes]
rs852407	0.88[ASN][1000 genomes]
rs852408	0.94[ASN][1000 genomes]
rs852410	0.84[YRI][hapmap]
rs852411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852412	1.00[ASN][1000 genomes]
rs852413	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs852414	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852415	0.83[YRI][hapmap]
rs852416	1.00[ASN][1000 genomes]
rs852418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852419	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs852420	0.84[YRI][hapmap]
rs852437	1.00[ASN][1000 genomes]
rs852439	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852440	1.00[ASN][1000 genomes]
rs852442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852449	0.94[ASN][1000 genomes]
rs852451	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852455	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852458	1.00[ASN][1000 genomes]
rs852459	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852460	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852462	1.00[ASN][1000 genomes]
rs852465	1.00[ASN][1000 genomes]
rs852466	1.00[ASN][1000 genomes]
rs852467	1.00[ASN][1000 genomes]
rs852468	0.83[YRI][hapmap]
rs852469	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852474	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852475	1.00[ASN][1000 genomes]
rs852476	1.00[ASN][1000 genomes]
rs852477	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852487	1.00[ASN][1000 genomes]
rs852489	0.93[YRI][hapmap]
rs852490	1.00[ASN][1000 genomes]
rs852514	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852515	0.89[ASN][1000 genomes]
rs852518	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852521	1.00[ASN][1000 genomes]
rs852523	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs852524	1.00[ASN][1000 genomes]
rs852525	1.00[ASN][1000 genomes]
rs941016	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
5	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
6	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
7	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
8	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription 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	336 gene(s)	inside rSNPs	diseases
9	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
10	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
11	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
12	nsv1025434	chr7:5537571-5705283	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	297 gene(s)	inside rSNPs	diseases
13	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
14	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
15	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
16	nsv887414	chr7:5584934-5667645	Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
17	nsv887415	chr7:5584934-5675305	Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
18	nsv887416	chr7:5584934-5695259	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
19	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
20	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
21	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers 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	126 gene(s)	inside rSNPs	diseases
22	nsv1034883	chr7:5651680-5696147	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5636200-5662000	Weak transcription	Fetal Kidney	kidney
2	chr7:5638800-5671000	Weak transcription	Right Atrium	heart
3	chr7:5642800-5664800	Weak transcription	Hela-S3	cervix
4	chr7:5645000-5662000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:5645000-5662200	Weak transcription	GM12878-XiMat	blood
6	chr7:5645600-5662000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:5647000-5661600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:5647200-5661600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr7:5647200-5663000	Weak transcription	NH-A	brain
10	chr7:5647400-5662200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:5647600-5673200	Weak transcription	Fetal Brain Male	brain
12	chr7:5648600-5665200	Weak transcription	HMEC	breast
13	chr7:5649800-5661600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr7:5650000-5661800	Weak transcription	Fetal Thymus	thymus
15	chr7:5650000-5669600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:5650400-5665000	Weak transcription	K562	blood
17	chr7:5650600-5661800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr7:5650600-5661800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr7:5650800-5661800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:5650800-5662000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:5650800-5662000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:5653200-5662000	Weak transcription	HUVEC	blood vessel
23	chr7:5655600-5662600	Weak transcription	Stomach Mucosa	stomach
24	chr7:5655600-5673200	Weak transcription	Psoas Muscle	Psoas
25	chr7:5655800-5664000	Weak transcription	NHEK	skin
26	chr7:5655800-5665400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr7:5657000-5664400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr7:5657200-5662600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr7:5657400-5665600	Strong transcription	Fetal Intestine Small	intestine
30	chr7:5657600-5663800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr7:5657800-5664400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr7:5657800-5665200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:5658200-5664800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr7:5658200-5664800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr7:5658200-5666400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr7:5658400-5664400	Strong transcription	Osteobl	bone
37	chr7:5658400-5664800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr7:5658400-5665000	Strong transcription	Stomach Smooth Muscle	stomach
39	chr7:5658400-5665400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:5658400-5665600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:5658400-5666200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:5658600-5664600	Strong transcription	Fetal Intestine Large	intestine
43	chr7:5658600-5668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:5658800-5664400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr7:5659000-5662200	Genic enhancers	Fetal Muscle Leg	muscle
46	chr7:5659000-5662200	Strong transcription	Lung	lung
47	chr7:5659000-5662400	Genic enhancers	Fetal Muscle Trunk	muscle
48	chr7:5659000-5663800	Strong transcription	Brain Hippocampus Middle	brain
49	chr7:5659000-5664200	Strong transcription	NHLF	lung
50	chr7:5659000-5664600	Strong transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links