Variant report

Variant	rs60629297
Chromosome Location	chr12:48438290-48438291
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48428906..48431676-chr12:48435313..48438563,3	MCF-7	breast:
2	chr12:48433439..48436867-chr12:48436934..48440362,3	K562	blood:
3	chr12:48438068..48440402-chr12:48448610..48451360,2	K562	blood:
4	chr12:48383628..48385806-chr12:48436712..48438837,2	K562	blood:
5	chr12:48431984..48434939-chr12:48438010..48440362,2	K562	blood:

Variant related genes	Relation type
ENSG00000240399	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1018973	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783227	0.81[EUR][1000 genomes]
rs11612578	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11612970	0.85[EUR][1000 genomes]
rs11613485	0.86[EUR][1000 genomes]
rs12580764	0.88[EUR][1000 genomes]
rs12581972	0.82[EUR][1000 genomes]
rs1476608	0.84[EUR][1000 genomes]
rs17122565	0.82[ASN][1000 genomes]
rs17122611	0.88[EUR][1000 genomes]
rs17122612	0.88[EUR][1000 genomes]
rs17122613	0.86[EUR][1000 genomes]
rs17122651	0.84[EUR][1000 genomes]
rs1859441	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs1859444	0.80[EUR][1000 genomes]
rs1968071	0.84[EUR][1000 genomes]
rs1990029	0.86[EUR][1000 genomes]
rs2286022	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3742074	0.88[EUR][1000 genomes]
rs3803183	0.81[EUR][1000 genomes]
rs3803184	0.81[EUR][1000 genomes]
rs3825404	0.81[EUR][1000 genomes]
rs4293182	0.86[EUR][1000 genomes]
rs4589362	0.84[EUR][1000 genomes]
rs4760611	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760614	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760615	0.91[EUR][1000 genomes]
rs4760618	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4760677	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57054831	0.84[EUR][1000 genomes]
rs57380031	0.86[EUR][1000 genomes]
rs58046797	0.84[EUR][1000 genomes]
rs59766465	0.87[EUR][1000 genomes]
rs60567660	0.84[EUR][1000 genomes]
rs60681522	0.88[EUR][1000 genomes]
rs6580647	0.87[EUR][1000 genomes]
rs6580649	0.84[EUR][1000 genomes]
rs6580651	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132668	0.84[EUR][1000 genomes]
rs7133249	0.88[EUR][1000 genomes]
rs72644841	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72644842	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72644843	0.88[EUR][1000 genomes]
rs72644844	0.88[EUR][1000 genomes]
rs7296913	0.84[EUR][1000 genomes]
rs7305954	0.85[EUR][1000 genomes]
rs7310579	0.91[EUR][1000 genomes]
rs7312326	0.84[EUR][1000 genomes]
rs7957764	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7959755	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963934	0.84[EUR][1000 genomes]
rs7967762	0.87[EUR][1000 genomes]
rs7971668	0.88[EUR][1000 genomes]
rs9651993	0.86[EUR][1000 genomes]
rs9805048	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60629297	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48431400-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:48431800-48438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:48431800-48438400	Weak transcription	K562	blood
5	chr12:48431800-48438800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:48431800-48456600	Weak transcription	NHLF	lung
7	chr12:48432000-48438400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:48432000-48438400	Weak transcription	Fetal Kidney	kidney
9	chr12:48432000-48438400	Weak transcription	Ovary	ovary
10	chr12:48432000-48438800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr12:48432000-48438800	Weak transcription	NHDF-Ad	bronchial
12	chr12:48432000-48439800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:48432000-48439800	Weak transcription	Fetal Heart	heart
14	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:48432200-48438400	Weak transcription	HepG2	liver
16	chr12:48432200-48438400	Weak transcription	HSMMtube	muscle
17	chr12:48432200-48438600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:48433200-48438600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:48433400-48438800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:48433800-48438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:48434400-48439200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:48434800-48438400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr12:48434800-48438400	Weak transcription	Brain Substantia Nigra	brain
25	chr12:48434800-48438400	Weak transcription	Esophagus	oesophagus
26	chr12:48434800-48438400	Weak transcription	Psoas Muscle	Psoas
27	chr12:48434800-48438600	Weak transcription	A549	lung
28	chr12:48435000-48438400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48435000-48438400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:48435200-48438600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:48435200-48445600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
33	chr12:48435400-48438400	Weak transcription	Osteobl	bone
34	chr12:48435400-48444600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:48435600-48438800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:48435600-48444800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:48435600-48445800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr12:48435800-48438400	Weak transcription	HUVEC	blood vessel
40	chr12:48435800-48438600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:48435800-48444600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr12:48435800-48445800	Strong transcription	Primary B cells from cord blood	blood
43	chr12:48435800-48452400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr12:48436000-48438600	Weak transcription	Fetal Brain Male	brain
45	chr12:48436000-48438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:48436000-48445000	Strong transcription	Fetal Muscle Leg	muscle
47	chr12:48436000-48445800	Strong transcription	Fetal Thymus	thymus
48	chr12:48436000-48448200	Strong transcription	Primary T cells from cord blood	blood
49	chr12:48436200-48438400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr12:48436200-48444600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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