Variant report

Variant	rs10941604
Chromosome Location	chr5:42996445-42996446
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:42990996..42996897-chr5:43036694..43045949,13	K562	blood:
2	chr5:42996039..42998077-chr5:43007869..43010510,2	MCF-7	breast:
3	chr5:42988028..42998045-chr5:43036469..43045844,20	K562	blood:
4	chr5:42989723..42997135-chr5:43060250..43070296,19	K562	blood:
5	chr5:42990973..42999044-chr5:43062393..43068169,17	K562	blood:
6	chr5:42989588..43001279-chr5:43004636..43014428,32	K562	blood:
7	chr5:42994652..42996871-chr5:43105565..43107104,2	K562	blood:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000272144	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10064003	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10522	0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10941605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747435	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747714	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11958008	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12697439	0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13169690	0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13170208	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13171133	0.84[ASN][1000 genomes]
rs13178479	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13179934	0.90[ASN][1000 genomes]
rs1542369	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1574407	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs160709	0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1618891	0.86[JPT][hapmap]
rs1624415	0.86[JPT][hapmap]
rs178415	0.95[JPT][hapmap]
rs186323	0.86[ASN][1000 genomes]
rs186324	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1902101	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2100473	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124069	0.90[ASN][1000 genomes]
rs222060	0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253450	0.87[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329994	0.87[ASN][1000 genomes]
rs2329995	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2548334	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2548336	0.88[CHB][hapmap]
rs2548339	0.86[ASN][1000 genomes]
rs2548341	0.83[ASN][1000 genomes]
rs2548343	0.84[ASN][1000 genomes]
rs2548345	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548346	0.85[ASN][1000 genomes]
rs2548349	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2548350	0.81[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2548353	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548356	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603620	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2603644	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2603656	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882295	0.89[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs309909	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs309914	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs309922	0.83[ASN][1000 genomes]
rs309923	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs309924	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs309925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs309926	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs309927	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs309948	0.82[ASN][1000 genomes]
rs309950	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs316395	0.87[ASN][1000 genomes]
rs316396	0.81[ASN][1000 genomes]
rs316404	0.95[JPT][hapmap]
rs316408	0.95[JPT][hapmap]
rs316413	0.95[JPT][hapmap]
rs316414	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316416	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs316419	0.87[ASN][1000 genomes]
rs316422	0.87[ASN][1000 genomes]
rs3909456	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4033115	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4092293	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4092294	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4296812	0.84[ASN][1000 genomes]
rs512921	0.87[JPT][hapmap]
rs557076	0.86[JPT][hapmap]
rs567884	0.86[JPT][hapmap]
rs613825	0.87[ASN][1000 genomes]
rs643307	0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451660	0.84[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6451661	0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6451662	0.83[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875214	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6879130	0.95[JPT][hapmap]
rs6892422	0.86[JPT][hapmap]
rs724430	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs768441	0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7715065	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs782971	0.86[JPT][hapmap]
rs782978	0.86[JPT][hapmap]
rs782984	0.86[JPT][hapmap]
rs903391	0.86[JPT][hapmap]
rs9292862	0.95[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
11	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
12	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
13	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
14	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
15	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
16	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10941604	FLJ32255	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42995000-43000000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:42995000-43000400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:42995400-42997000	Flanking Active TSS	Dnd41	blood
4	chr5:42995600-42999600	Weak transcription	NHEK	skin
5	chr5:42995600-42999800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:42995600-43000000	Weak transcription	HMEC	breast
7	chr5:42995800-42996600	Enhancers	HepG2	liver
8	chr5:42995800-42996600	Enhancers	Osteobl	bone
9	chr5:42995800-42996800	Enhancers	NHLF	lung
10	chr5:42995800-42997000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:42995800-42998800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:42995800-43000000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:42995800-43000000	Weak transcription	K562	blood
14	chr5:42995800-43000200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr5:42995800-43000200	Weak transcription	Placenta	Placenta
16	chr5:42996000-42996600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr5:42996000-42996600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:42996000-42996800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:42996000-42996800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:42996000-42996800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:42996000-42996800	Enhancers	Hela-S3	cervix
22	chr5:42996000-42997000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr5:42996000-42997000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:42996000-42997000	Enhancers	HUVEC	blood vessel
25	chr5:42996000-42997200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr5:42996000-42997200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr5:42996000-42997200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr5:42996000-42997400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:42996000-42997400	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:42996000-42999200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:42996000-42999200	Weak transcription	Primary B cells from cord blood	blood
32	chr5:42996000-42999800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:42996000-43000000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:42996000-43000200	Weak transcription	Thymus	Thymus
35	chr5:42996000-43000800	Weak transcription	Spleen	Spleen
36	chr5:42996200-42996600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:42996200-42996600	Flanking Active TSS	A549	lung
38	chr5:42996200-42996800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr5:42996200-42997000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:42996200-43000000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:42996200-43000000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:42996400-42996600	Flanking Active TSS	NHDF-Ad	bronchial
43	chr5:42996400-42996800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:42996400-42997200	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr5:42996400-42999800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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