Variant report

Variant	rs7971668
Chromosome Location	chr12:48469696-48469697
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48468414..48470929-chr12:48522430..48524635,2	K562	blood:
2	chr12:48468062..48470836-chr12:48471643..48474168,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1018973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10492080	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783227	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs10783231	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10783232	0.81[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs10875742	0.86[ASN][1000 genomes]
rs11168451	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs11168455	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs11609399	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11612578	0.94[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs11612970	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11613485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11613781	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12580764	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12581972	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12822085	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1476608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17122565	0.95[JPT][hapmap]
rs17122611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs17122613	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1859441	0.93[CEU][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes]
rs1859444	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1968071	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];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1990029	0.87[EUR][1000 genomes]
rs2286022	0.87[EUR][1000 genomes]
rs3742074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs3803183	0.82[EUR][1000 genomes]
rs3803184	0.82[EUR][1000 genomes]
rs3825404	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4075913	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4141065	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4293182	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4589362	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760611	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs4760614	0.94[EUR][1000 genomes]
rs4760615	0.92[EUR][1000 genomes]
rs4760618	0.90[EUR][1000 genomes]
rs4760620	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs4760677	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4760683	0.81[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4760685	1.00[JPT][hapmap]
rs4760692	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4760698	0.81[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs57054831	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57380031	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57655233	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58046797	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58331734	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59766465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60567660	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60629297	0.88[EUR][1000 genomes]
rs60681522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580647	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs6580649	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs6580651	0.94[EUR][1000 genomes]
rs6580656	0.87[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap]
rs6580660	1.00[JPT][hapmap]
rs7132668	0.85[EUR][1000 genomes]
rs7133249	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726354	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644841	0.91[EUR][1000 genomes]
rs72644842	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644845	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72644846	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72644847	0.87[EUR][1000 genomes]
rs7296913	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];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7305954	0.86[EUR][1000 genomes]
rs7310579	0.92[EUR][1000 genomes]
rs7312326	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7315258	0.87[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7485057	1.00[JPT][hapmap]
rs7485824	0.80[EUR][1000 genomes]
rs757556	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7957764	0.92[EUR][1000 genomes]
rs7959755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967762	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7969749	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs879242	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9651993	0.87[EUR][1000 genomes]
rs9805048	0.86[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
rs7971668	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
5	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:48444200-48474600	Weak transcription	Gastric	stomach
7	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
8	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:48453600-48469800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:48453600-48471200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
14	chr12:48454800-48472000	Strong transcription	Dnd41	blood
15	chr12:48457400-48482000	Weak transcription	Right Ventricle	heart
16	chr12:48457600-48478600	Weak transcription	HSMMtube	muscle
17	chr12:48459200-48479000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:48460800-48469800	Strong transcription	Primary T cells from cord blood	blood
19	chr12:48463000-48469800	Strong transcription	Primary B cells from cord blood	blood
20	chr12:48463600-48476200	Weak transcription	HUVEC	blood vessel
21	chr12:48464400-48476200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:48464600-48472600	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48464600-48489400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:48464800-48476000	Weak transcription	Fetal Brain Male	brain
25	chr12:48464800-48482400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:48465000-48474000	Weak transcription	Lung	lung
27	chr12:48465000-48474600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:48465000-48477000	Weak transcription	Brain Angular Gyrus	brain
29	chr12:48465000-48478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr12:48465000-48478800	Weak transcription	Aorta	Aorta
31	chr12:48465000-48487400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr12:48465800-48476800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:48466200-48481400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:48466400-48472600	Weak transcription	Ovary	ovary
35	chr12:48466800-48470000	Weak transcription	Left Ventricle	heart
36	chr12:48466800-48472600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:48466800-48472600	Weak transcription	Fetal Stomach	stomach
38	chr12:48466800-48478800	Weak transcription	Esophagus	oesophagus
39	chr12:48468200-48472400	Weak transcription	NHLF	lung
40	chr12:48468200-48472600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:48468200-48472600	Weak transcription	Hela-S3	cervix
42	chr12:48468200-48476000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:48468200-48476000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:48468200-48476000	Weak transcription	HSMM	muscle
45	chr12:48468200-48478800	Weak transcription	HepG2	liver
46	chr12:48468400-48471000	Weak transcription	Stomach Smooth Muscle	stomach
47	chr12:48468400-48471400	Weak transcription	Fetal Brain Female	brain
48	chr12:48468400-48472600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:48468400-48472600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:48468400-48474000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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