Variant report

Variant	rs590460
Chromosome Location	chr12:50449976-50449977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr12:50449924-50450097	K562	blood:	n/a	n/a
2	YY1	chr12:50449814-50450048	GM12891	blood:	n/a	n/a
3	CTCF	chr12:50449832-50450100	MCF-7	breast:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
4	CTCF	chr12:50449880-50450030	HepG2	liver:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
5	CTCF	chr12:50449900-50450050	GM12872	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
6	CTCF	chr12:50449643-50450121	Spleen_OC	spleen:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
7	PAX5	chr12:50449786-50450092	GM12878	blood:	n/a	n/a
8	MAX	chr12:50449532-50450138	H1-hESC	embryonic stem cell:	n/a	n/a
9	RAD21	chr12:50449465-50450201	HCT-116	colon:	n/a	chr12:50449936-50449955
10	CTCF	chr12:50449900-50450050	GM12875	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
11	RAD21	chr12:50449677-50450173	A549	lung:	n/a	chr12:50449936-50449955
12	CTCF	chr12:50449840-50449990	WI-38	lung:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
13	CBX3	chr12:50449601-50450085	K562	blood:	n/a	n/a
14	RAD21	chr12:50449701-50450161	HepG2	liver:	n/a	chr12:50449936-50449955
15	CUX1	chr12:50449783-50450067	K562	blood:	n/a	n/a
16	ZNF143	chr12:50449735-50450133	GM12878	blood:	n/a	n/a
17	MAX	chr12:50449488-50450216	A549	lung:	n/a	n/a
18	CTCF	chr12:50449860-50450010	GM12873	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
19	CTCF	chr12:50449900-50450050	HepG2	liver:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
20	RAD21	chr12:50449212-50450384	SK-N-SH	brain:	n/a	chr12:50449346-50449353 chr12:50449936-50449955 chr12:50450313-50450320
21	CTCF	chr12:50449900-50450050	GM12866	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
22	CTCF	chr12:50449742-50450120	T-47D	breast:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
23	CTCF	chr12:50449860-50450010	HUVEC	blood vessel:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
24	REST	chr12:50449730-50450238	PFSK-1	brain:	n/a	n/a
25	CTCF	chr12:50449290-50450462	HCT-116	colon:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
26	CTCF	chr12:50449824-50450110	H1-hESC	embryonic stem cell:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
27	CTCF	chr12:50449511-50450097	K562	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
28	CTCF	chr12:50449860-50450010	GM12878	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
29	CTCF	chr12:50449764-50450134	GM12892	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
30	CTCF	chr12:50449880-50450030	GM12866	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
31	MAZ	chr12:50449757-50450073	HepG2	liver:	n/a	n/a
32	RAD21	chr12:50449751-50450119	K562	blood:	n/a	chr12:50449936-50449955
33	MXI1	chr12:50449576-50450015	GM12878	blood:	n/a	n/a
34	CTCF	chr12:50449840-50449990	GM12870	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
35	CTCF	chr12:50449666-50450082	A549	lung:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
36	MYC	chr12:50449564-50450068	MCF10A-Er-Src	breast:	n/a	n/a
37	CTCF	chr12:50449811-50450125	Pancreas_OC	pancreas:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
38	CTCF	chr12:50449860-50450010	HEK293	kidney:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
39	CTCF	chr12:50449880-50450030	HBMEC	blood vessel:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
40	CTCF	chr12:50449715-50450113	SK-N-SH_RA	brain:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
41	BACH1	chr12:50449749-50450056	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr12:50449802-50450097	GM13977	blood:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
43	REST	chr12:50449830-50450068	U87	brain:	n/a	n/a
44	REST	chr12:50449781-50450114	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr12:50449880-50450030	HCT-116	colon:	n/a	chr12:50449938-50449956 chr12:50449933-50449954
46	TEAD4	chr12:50449629-50449996	K562	blood:	n/a	n/a
47	RAD21	chr12:50449711-50450118	HepG2	liver:	n/a	chr12:50449936-50449955
48	GTF2F1	chr12:50449765-50450137	H1-hESC	embryonic stem cell:	n/a	n/a
49	RAD21	chr12:50449569-50450189	HepG2	liver:	n/a	chr12:50449936-50449955
50	CTCF	chr12:50449570-50450176	H1-hESC	embryonic stem cell:	n/a	chr12:50449938-50449956 chr12:50449933-50449954

No.	Distal block	Cell Line	Cell type
1	chr12:50260411..50261384-chr12:50449745..50450389,4	MCF-7	breast:
2	chr12:50432763..50433687-chr12:50449544..50450364,3	MCF-7	breast:
3	chr12:50432725..50434312-chr12:50449330..50450437,10	MCF-7	breast:
4	chr12:50368102..50368945-chr12:50449516..50450250,3	K562	blood:
5	chr12:50415480..50421111-chr12:50448192..50451032,5	K562	blood:
6	chr12:50358701..50362803-chr12:50449341..50451682,4	MCF-7	breast:
7	chr12:50369533..50370611-chr12:50449444..50450226,3	MCF-7	breast:
8	chr12:50415480..50418292-chr12:50448192..50450079,2	K562	blood:
9	chr12:50367707..50368705-chr12:50449431..50450774,7	MCF-7	breast:
10	chr12:50360514..50361964-chr12:50449435..50451127,13	K562	blood:
11	chr12:50360482..50361451-chr12:50449730..50450389,4	MCF-7	breast:
12	chr12:50449658..50451557-chr12:50467280..50470251,2	MCF-7	breast:
13	chr12:50360496..50362709-chr12:50448964..50450845,14	MCF-7	breast:
14	chr12:50449562..50451220-chr12:50537075..50538581,2	K562	blood:
15	chr12:50432739..50435190-chr12:50449417..50450489,14	K562	blood:
16	chr12:50347500..50349334-chr12:50448823..50450713,2	MCF-7	breast:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000161800	Chromatin interaction
ENSG00000110881	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10875995	0.92[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs10875996	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169270	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs376184	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs386469	0.87[ASN][1000 genomes]
rs393848	0.81[ASN][1000 genomes]
rs404751	0.89[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs439171	0.80[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs450423	0.80[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs484951	0.80[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4898546	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs56990521	0.91[EUR][1000 genomes]
rs613066	0.80[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs627869	0.89[ASN][1000 genomes]
rs627887	0.89[ASN][1000 genomes]
rs653576	0.90[ASN][1000 genomes]
rs685012	0.83[ASW][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs706789	0.80[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs706794	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73299515	0.87[EUR][1000 genomes]
rs73299518	0.89[EUR][1000 genomes]
rs7956491	0.87[EUR][1000 genomes]
rs835591	0.92[ASN][1000 genomes]
rs835593	0.95[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs835594	0.83[ASN][1000 genomes]
rs836175	0.81[AMR][1000 genomes]
rs836178	0.92[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs836184	0.89[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs836185	0.91[ASN][1000 genomes]
rs836186	0.87[ASN][1000 genomes]
rs844359	0.95[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs860699	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs590460	LASS5	cis	parietal	SCAN
rs590460	AQP6	cis	parietal	SCAN
rs590460	CERS5	cis	Nerve Tibial	GTEx
rs590460	ATF1	cis	parietal	SCAN
rs590460	SNORA2A	cis	parietal	SCAN
rs590460	SLC38A1	cis	parietal	SCAN
rs590460	LASS5	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50444400-50450800	Weak transcription	Lung	lung
2	chr12:50444800-50450800	Weak transcription	Right Atrium	heart
3	chr12:50445400-50450000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:50449400-50450000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:50449400-50450600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50449400-50450600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr12:50449400-50450600	Enhancers	Fetal Brain Male	brain
8	chr12:50449400-50450600	Bivalent Enhancer	Fetal Stomach	stomach
9	chr12:50449400-50450600	Bivalent Enhancer	Stomach Mucosa	stomach
10	chr12:50449400-50450800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:50449400-50450800	Bivalent Enhancer	Fetal Lung	lung
12	chr12:50449600-50450000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
13	chr12:50449600-50450000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
16	chr12:50449600-50450000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
17	chr12:50449600-50450000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr12:50449600-50450000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
21	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:50449600-50450000	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:50449600-50450000	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
24	chr12:50449600-50450000	Flanking Active TSS	K562	blood
25	chr12:50449600-50450000	Flanking Active TSS	NHEK	skin
26	chr12:50449600-50450200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
27	chr12:50449600-50450200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:50449600-50450200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:50449600-50450200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr12:50449600-50450200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:50449600-50450200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:50449600-50450200	Flanking Active TSS	Colon Smooth Muscle	Colon
33	chr12:50449600-50450400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
34	chr12:50449600-50450400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:50449600-50450400	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:50449600-50450400	Enhancers	Brain Substantia Nigra	brain
37	chr12:50449600-50450400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
38	chr12:50449600-50450400	Enhancers	Esophagus	oesophagus
39	chr12:50449600-50450400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr12:50449600-50450400	Flanking Active TSS	Hela-S3	cervix
41	chr12:50449600-50450600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:50449600-50450600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:50449600-50450600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:50449600-50450600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
45	chr12:50449600-50450600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr12:50449600-50450600	Bivalent Enhancer	Adipose Nuclei	Adipose
47	chr12:50449600-50450600	Bivalent Enhancer	Colonic Mucosa	Colon
48	chr12:50449600-50450600	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
49	chr12:50449600-50450600	Enhancers	Fetal Heart	heart
50	chr12:50449600-50450600	Bivalent Enhancer	Fetal Intestine Small	intestine

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