Variant report

Variant	rs4760677
Chromosome Location	chr12:48449163-48449164
allele	C/T
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	ZNF274	chr12:48448996-48450212	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48446661..48450217-chr12:48458596..48461556,3	K562	blood:
2	chr12:48448475..48449474-chr5:40834158..40834864,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP1-228P16.5.1-2	chr12:48448596-48449374	NONHSAT027976

Variant related genes	Relation type
ENSG00000240399	TF binding region
ENSG00000145592	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1018973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492080	0.83[EUR][1000 genomes]
rs10783226	0.83[EUR][1000 genomes]
rs10783227	0.88[EUR][1000 genomes]
rs11609399	0.83[EUR][1000 genomes]
rs11612578	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11612970	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11613485	0.92[EUR][1000 genomes]
rs11613781	0.83[EUR][1000 genomes]
rs12580764	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12581972	0.87[EUR][1000 genomes]
rs1476608	0.89[EUR][1000 genomes]
rs1635526	0.81[EUR][1000 genomes]
rs17122565	0.81[ASN][1000 genomes]
rs17122611	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122612	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122613	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17122651	0.89[EUR][1000 genomes]
rs1793931	0.83[EUR][1000 genomes]
rs1793933	0.83[EUR][1000 genomes]
rs1859441	0.97[EUR][1000 genomes]
rs1859444	0.87[EUR][1000 genomes]
rs1968071	0.89[EUR][1000 genomes]
rs1990029	0.92[EUR][1000 genomes]
rs2286022	0.93[EUR][1000 genomes]
rs3742074	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3803183	0.88[EUR][1000 genomes]
rs3803184	0.88[EUR][1000 genomes]
rs3825404	0.88[EUR][1000 genomes]
rs4141065	0.81[EUR][1000 genomes]
rs4293182	0.92[EUR][1000 genomes]
rs4589362	0.89[EUR][1000 genomes]
rs4760611	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760614	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760615	0.98[EUR][1000 genomes]
rs4760618	0.95[EUR][1000 genomes]
rs57054831	0.89[EUR][1000 genomes]
rs57380031	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57655233	0.81[EUR][1000 genomes]
rs58046797	0.89[EUR][1000 genomes]
rs58331734	0.83[EUR][1000 genomes]
rs59766465	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60567660	0.89[EUR][1000 genomes]
rs60629297	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60681522	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580647	0.93[EUR][1000 genomes]
rs6580649	0.91[EUR][1000 genomes]
rs6580651	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7132668	0.91[EUR][1000 genomes]
rs7133249	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs726354	0.83[EUR][1000 genomes]
rs72644841	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72644842	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72644843	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644844	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72644845	0.83[EUR][1000 genomes]
rs72644847	0.81[EUR][1000 genomes]
rs7296913	0.89[EUR][1000 genomes]
rs7305954	0.91[EUR][1000 genomes]
rs7310579	0.98[EUR][1000 genomes]
rs7312326	0.89[EUR][1000 genomes]
rs757556	0.83[EUR][1000 genomes]
rs7957764	0.98[EUR][1000 genomes]
rs7959755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963934	0.89[EUR][1000 genomes]
rs7967762	0.93[EUR][1000 genomes]
rs7971668	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs879242	0.83[EUR][1000 genomes]
rs9651993	0.92[EUR][1000 genomes]
rs9805048	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	esv3339510	chr12:48448935-48452108	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4760677	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48431800-48456600	Weak transcription	NHLF	lung
2	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
5	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:48435800-48452400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr12:48439200-48453000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:48439200-48456800	Weak transcription	HMEC	breast
10	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:48439600-48455400	Weak transcription	Colonic Mucosa	Colon
12	chr12:48440000-48452200	Weak transcription	NHDF-Ad	bronchial
13	chr12:48440000-48454000	Weak transcription	HUVEC	blood vessel
14	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:48440200-48452600	Weak transcription	Brain Germinal Matrix	brain
16	chr12:48440200-48452600	Weak transcription	Right Ventricle	heart
17	chr12:48440200-48453800	Weak transcription	Colon Smooth Muscle	Colon
18	chr12:48440400-48453400	Weak transcription	Esophagus	oesophagus
19	chr12:48440800-48452400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:48440800-48452400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:48441000-48452600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr12:48441200-48452400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48441200-48457000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr12:48441400-48452400	Weak transcription	Brain Anterior Caudate	brain
25	chr12:48441400-48453400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48441400-48453400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:48441400-48454400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
29	chr12:48441600-48452200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:48441600-48452400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:48441600-48452400	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr12:48441600-48452800	Weak transcription	NHEK	skin
33	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:48442000-48452200	Weak transcription	Fetal Brain Female	brain
35	chr12:48442000-48452400	Weak transcription	Fetal Kidney	kidney
36	chr12:48442200-48452400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr12:48442400-48452600	Weak transcription	Fetal Brain Male	brain
38	chr12:48442800-48452400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:48443000-48452200	Weak transcription	HepG2	liver
40	chr12:48443000-48452200	Weak transcription	NH-A	brain
41	chr12:48443000-48453200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:48443200-48452400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:48443400-48452000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr12:48443400-48452200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:48443400-48452400	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr12:48443400-48452400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:48443400-48453400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:48443400-48453600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr12:48443600-48452400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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