Variant report

Variant	rs7974480
Chromosome Location	chr12:50798335-50798336
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50797616..50799826-chr12:50802454..50804004,2	K562	blood:
2	chr12:50794762..50796457-chr12:50796893..50799781,4	K562	blood:
3	chr12:50792642..50794335-chr12:50796337..50798839,2	MCF-7	breast:
4	chr12:50793078..50796292-chr12:50797637..50799893,4	K562	blood:
5	chr12:50797471..50799671-chr12:50813461..50817013,3	K562	blood:

Variant related genes	Relation type
ENSG00000161813	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10506293	1.00[ASW][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747580	0.93[ASN][1000 genomes]
rs10747581	0.93[ASN][1000 genomes]
rs10783348	0.91[MEX][hapmap]
rs10783362	0.86[CHB][hapmap];0.81[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10783368	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs10876030	0.85[ASN][1000 genomes]
rs10876034	0.86[ASN][1000 genomes]
rs10876048	0.85[EUR][1000 genomes]
rs10876054	0.85[EUR][1000 genomes]
rs11169408	0.85[ASN][1000 genomes]
rs11169422	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169427	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11169440	0.86[ASN][1000 genomes]
rs12099511	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12099615	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs12296379	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12307602	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12320201	0.85[EUR][1000 genomes]
rs12578525	0.88[ASN][1000 genomes]
rs13328926	0.90[EUR][1000 genomes]
rs1402693	0.90[EUR][1000 genomes]
rs17119774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17119778	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17124672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17531020	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996750	0.90[EUR][1000 genomes]
rs2684902	0.85[EUR][1000 genomes]
rs28414775	0.90[EUR][1000 genomes]
rs28479152	0.90[EUR][1000 genomes]
rs2947617	0.85[EUR][1000 genomes]
rs4129355	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4238104	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs4257057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4298982	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4306347	0.90[EUR][1000 genomes]
rs4351895	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4450234	0.89[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4517607	0.90[EUR][1000 genomes]
rs4562889	1.00[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4768877	0.92[ASN][1000 genomes]
rs4768878	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4768879	0.88[ASN][1000 genomes]
rs4768880	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4768887	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768928	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4768936	0.93[ASN][1000 genomes]
rs56150799	0.81[AMR][1000 genomes]
rs56671180	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56753963	0.90[EUR][1000 genomes]
rs56989201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57283487	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57293958	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57512759	0.90[EUR][1000 genomes]
rs57578212	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57811009	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57828015	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58500867	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58869591	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58888905	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58915267	0.94[EUR][1000 genomes]
rs58916974	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59163743	0.85[AMR][1000 genomes]
rs59194948	0.90[EUR][1000 genomes]
rs59683461	0.90[EUR][1000 genomes]
rs59696942	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59968707	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60010359	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60198651	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60201334	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60239257	0.90[EUR][1000 genomes]
rs60242613	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60396677	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60420087	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60494920	0.90[EUR][1000 genomes]
rs60610745	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60743903	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61578731	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6580745	0.81[AMR][1000 genomes]
rs6580753	0.88[ASN][1000 genomes]
rs6580754	0.87[ASN][1000 genomes]
rs7131993	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7133488	0.96[ASN][1000 genomes]
rs7135159	0.92[ASN][1000 genomes]
rs7135222	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7138063	0.86[ASN][1000 genomes]
rs7295610	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs7296212	1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7299321	0.96[ASN][1000 genomes]
rs7301125	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7302749	0.85[EUR][1000 genomes]
rs7304017	0.86[ASN][1000 genomes]
rs7304262	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7306387	0.90[EUR][1000 genomes]
rs74090120	0.86[AMR][1000 genomes]
rs7487645	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7953880	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.90[EUR][1000 genomes]
rs7955176	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7955310	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7957033	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs7965165	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7978443	0.90[EUR][1000 genomes]
rs7978625	0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[ASN][1000 genomes]
rs7979184	0.84[EUR][1000 genomes]
rs9634264	1.00[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv1041563	chr12:50705715-50861699	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1049665	chr12:50705715-50871542	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv899076	chr12:50770291-50869589	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
8	nsv469376	chr12:50792846-50856613	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
9	nsv558841	chr12:50792846-50856613	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
10	nsv470291	chr12:50792846-50858820	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50795400-50819400	Weak transcription	Spleen	Spleen
2	chr12:50795600-50802600	Weak transcription	Gastric	stomach
3	chr12:50795800-50798600	Weak transcription	Lung	lung
4	chr12:50795800-50799000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:50796000-50809400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:50796000-50809600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:50796000-50812400	Weak transcription	Esophagus	oesophagus
8	chr12:50796000-50819400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:50796400-50802600	Weak transcription	Small Intestine	intestine
10	chr12:50796600-50798400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:50796600-50798800	Enhancers	Stomach Mucosa	stomach
12	chr12:50796600-50809800	Weak transcription	Thymus	Thymus
13	chr12:50796800-50801800	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:50796800-50808400	Weak transcription	Fetal Thymus	thymus
15	chr12:50796800-50809600	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:50796800-50810000	Weak transcription	Aorta	Aorta
17	chr12:50796800-50823200	Weak transcription	HSMMtube	muscle
18	chr12:50796800-50824000	Weak transcription	Fetal Brain Female	brain
19	chr12:50796800-50832600	Weak transcription	Brain Substantia Nigra	brain
20	chr12:50797000-50798400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:50797000-50798400	Enhancers	Colon Smooth Muscle	Colon
22	chr12:50797000-50798400	Enhancers	Fetal Kidney	kidney
23	chr12:50797000-50798400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:50797000-50799000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:50797000-50800200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:50797000-50801400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:50797000-50807200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:50797000-50809600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:50797000-50809600	Weak transcription	Fetal Intestine Large	intestine
30	chr12:50797000-50809800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr12:50797000-50809800	Weak transcription	HSMM	muscle
32	chr12:50797000-50821800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:50797000-50822200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr12:50797000-50822600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:50797200-50798400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr12:50797200-50798400	Enhancers	Hela-S3	cervix
37	chr12:50797200-50798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:50797200-50799200	Enhancers	HepG2	liver
39	chr12:50797200-50800600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:50797200-50801600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr12:50797200-50802200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr12:50797200-50802800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:50797200-50806200	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:50797200-50808000	Weak transcription	Primary T cells from cord blood	blood
45	chr12:50797200-50808000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:50797200-50809400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr12:50797200-50809800	Weak transcription	Colonic Mucosa	Colon
48	chr12:50797200-50810400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:50797200-50823800	Weak transcription	NH-A	brain
50	chr12:50797400-50798400	Enhancers	Dnd41	blood

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