Variant report

Variant	rs1258022
Chromosome Location	chr1:47055339-47055340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr1:47054732-47055747	GM08714	blood:	n/a	n/a
2	ZNF274	chr1:47054680-47056209	K562	blood:	n/a	n/a
3	ZNF274	chr1:47054751-47055933	NT2-D1	testis:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:47052682..47056987-chr1:47061043..47065460,4	K562	blood:
2	chr1:47054632..47056967-chr1:47067428..47069828,2	K562	blood:
3	chr1:47054104..47055847-chr1:47061988..47063605,2	K562	blood:
4	chr1:47050140..47053045-chr1:47054326..47056761,2	MCF-7	breast:
5	chr1:47046909..47051901-chr1:47054352..47058078,4	K562	blood:
6	chr1:47053959..47056132-chr1:47066697..47069062,3	K562	blood:
7	chr1:47053775..47056193-chr1:47067460..47069823,2	MCF-7	breast:
8	chr1:47040255..47042564-chr1:47053834..47056327,2	K562	blood:
9	chr1:47052104..47053858-chr1:47055220..47057402,2	K562	blood:

No data

Variant related genes	Relation type
MKNK1	TF binding region
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10890406	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs11211324	1.00[CHB][hapmap]
rs11211325	1.00[CHB][hapmap]
rs11801744	1.00[TSI][hapmap]
rs12060644	1.00[EUR][1000 genomes]
rs1258010	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258012	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258042	1.00[GIH][hapmap]
rs1258050	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1258051	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1258058	1.00[TSI][hapmap]
rs1258072	1.00[TSI][hapmap]
rs1273237	1.00[TSI][hapmap]
rs17102252	1.00[GIH][hapmap]
rs1767598	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1767612	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1933932	1.00[TSI][hapmap]
rs2241863	1.00[TSI][hapmap]
rs2241864	1.00[TSI][hapmap]
rs2274422	1.00[EUR][1000 genomes]
rs2476166	0.96[ASN][1000 genomes]
rs3737742	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3766218	1.00[TSI][hapmap]
rs4660357	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs57340268	1.00[EUR][1000 genomes]
rs57954022	1.00[EUR][1000 genomes]
rs58591480	1.00[EUR][1000 genomes]
rs60081306	1.00[EUR][1000 genomes]
rs629412	1.00[TSI][hapmap]
rs631368	1.00[TSI][hapmap]
rs631840	1.00[TSI][hapmap]
rs6660663	1.00[GIH][hapmap]
rs669647	1.00[TSI][hapmap]
rs723333	1.00[TSI][hapmap]
rs724309	1.00[TSI][hapmap]
rs736188	1.00[TSI][hapmap]
rs7525300	1.00[GIH][hapmap]
rs7549865	1.00[EUR][1000 genomes]
rs9094	1.00[TSI][hapmap]
rs942083	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs946321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active 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	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1009899	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv534954	chr1:47007765-47062737	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active 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	12 gene(s)	inside rSNPs	diseases
9	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47021000-47057000	Weak transcription	Fetal Brain Male	brain
2	chr1:47023200-47060000	Strong transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:47025600-47062400	Weak transcription	Fetal Heart	heart
4	chr1:47036000-47056400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:47036000-47060000	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:47037800-47057000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:47039200-47060400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:47039600-47060000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:47040200-47060400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:47042200-47057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr1:47042400-47057200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:47042600-47060400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:47042800-47056600	Weak transcription	Small Intestine	intestine
15	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr1:47046200-47056400	Weak transcription	NH-A	brain
18	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
19	chr1:47046400-47057200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:47047800-47060000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:47048000-47058000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:47048200-47056800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:47048600-47056400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:47049000-47056600	Weak transcription	Psoas Muscle	Psoas
26	chr1:47049200-47057000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:47049600-47056400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:47049600-47056800	Weak transcription	Brain Substantia Nigra	brain
29	chr1:47049600-47060400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:47050600-47068600	Weak transcription	NHDF-Ad	bronchial
31	chr1:47051000-47061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:47051400-47056600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:47051600-47059200	Strong transcription	HepG2	liver
34	chr1:47051600-47059800	Strong transcription	Primary B cells from peripheral blood	blood
35	chr1:47052000-47056800	Weak transcription	Colonic Mucosa	Colon
36	chr1:47052200-47057800	Strong transcription	Placenta	Placenta
37	chr1:47052200-47060000	Strong transcription	Liver	Liver
38	chr1:47052200-47060000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:47052400-47060000	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr1:47053200-47060200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:47054000-47056000	Weak transcription	Fetal Lung	lung
42	chr1:47054400-47058600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr1:47054400-47059000	Strong transcription	Aorta	Aorta
44	chr1:47054400-47059200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:47054400-47060000	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:47054400-47060000	Strong transcription	Fetal Thymus	thymus
47	chr1:47054400-47060000	Strong transcription	Lung	lung
48	chr1:47054400-47060000	Strong transcription	Thymus	Thymus
49	chr1:47054600-47055400	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:47054600-47055400	ZNF genes & repeats	GM12878-XiMat	blood

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