Variant report

Variant	rs10489770
Chromosome Location	chr1:46807597-46807598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ELF1	chr1:46807170-46807910	GM12878	blood:	n/a	n/a
2	MXI1	chr1:46805992-46808104	IMR90	lung:	n/a	n/a
3	CTCF	chr1:46807460-46807610	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:46807477-46808169	K562	blood:	n/a	n/a
5	POLR2A	chr1:46805002-46809990	K562	blood:	n/a	n/a
6	CTCF	chr1:46807460-46807610	GM12869	blood:	n/a	n/a
7	POLR2A	chr1:46805856-46808690	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:46807233-46808179	GM12878	blood:	n/a	n/a
9	WRNIP1	chr1:46805990-46808708	GM12878	blood:	n/a	n/a
10	CTCF	chr1:46807520-46807670	GM12867	blood:	n/a	n/a
11	CHD2	chr1:46807465-46808224	GM12878	blood:	n/a	n/a
12	JUN	chr1:46804251-46807834	K562	blood:	n/a	chr1:46806818-46806831
13	CTCF	chr1:46807460-46807610	GM12868	blood:	n/a	n/a
14	CTCF	chr1:46807580-46807730	GM12875	blood:	n/a	n/a
15	MXI1	chr1:46805301-46808164	SK-N-SH	brain:	n/a	n/a
16	HEY1	chr1:46807364-46808174	K562	blood:	n/a	n/a
17	POLR2A	chr1:46805936-46807820	K562	blood:	n/a	n/a
18	CTCF	chr1:46807540-46807690	Hela-S3	cervix:	n/a	n/a
19	EBF1	chr1:46807424-46809213	GM12878	blood:	n/a	n/a
20	RFX5	chr1:46807589-46807601	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46768190..46770861-chr1:46804850..46807772,3	MCF-7	breast:
2	chr1:46711990..46716191-chr1:46804369..46808176,4	K562	blood:
3	chr1:46649178..46652657-chr1:46804646..46808340,3	K562	blood:
4	chr1:46763061..46775715-chr1:46803221..46815018,50	K562	blood:
5	chr1:46763061..46775205-chr1:46803159..46817121,53	K562	blood:
6	chr1:46049506..46051127-chr1:46805584..46807919,2	K562	blood:
7	chr1:46775398..46777226-chr1:46806955..46809185,2	K562	blood:
8	chr1:46711469..46715741-chr1:46805142..46807635,4	K562	blood:

No data

Variant related genes	Relation type
NSUN4	TF binding region
ENSG00000173660	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117472	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10736428	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10789488	0.82[MEX][hapmap]
rs10890386	0.81[MEX][hapmap]
rs10890388	0.82[MEX][hapmap]
rs10890392	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028248	0.82[MEX][hapmap]
rs12029329	0.85[JPT][hapmap]
rs12126187	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs12141269	1.00[ASW][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs12406217	1.00[YRI][hapmap]
rs1547180	0.82[MEX][hapmap]
rs1571138	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs17102087	0.81[CHD][hapmap]
rs2145408	0.86[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap]
rs2295633	0.85[JPT][hapmap]
rs324418	0.82[CHD][hapmap];0.93[MEX][hapmap]
rs324420	0.82[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs4660918	0.82[MEX][hapmap]
rs4660919	0.82[MEX][hapmap]
rs4660921	0.82[MEX][hapmap]
rs6429600	0.84[JPT][hapmap]
rs6670926	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6689182	0.93[MEX][hapmap]
rs6696085	0.82[MEX][hapmap]
rs72677586	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs953070	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv470711	chr1:46660295-46810530	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv829748	chr1:46724508-46876122	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv947254	chr1:46769363-46808918	Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	esv12311	chr1:46805652-46810297	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv546162	chr1:46807597-46870761	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10489770	GPBP1L1	cis	parietal	SCAN
rs10489770	MMACHC	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46805000-46807600	Active TSS	A549	lung
2	chr1:46805200-46807600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:46805200-46807600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:46805200-46807600	Active TSS	Brain Cingulate Gyrus	brain
5	chr1:46805200-46807800	Active TSS	Colonic Mucosa	Colon
6	chr1:46805400-46807600	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:46805400-46807800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:46805600-46807600	Active TSS	Duodenum Mucosa	Duodenum
9	chr1:46805600-46808200	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:46805800-46807600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr1:46806600-46807600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:46806600-46807600	Flanking Active TSS	Dnd41	blood
13	chr1:46806800-46807600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr1:46806800-46807600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:46806800-46808000	Enhancers	Spleen	Spleen
16	chr1:46807000-46807600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
17	chr1:46807000-46807600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:46807000-46807600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:46807000-46807600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr1:46807000-46807600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:46807000-46807600	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:46807000-46807600	Flanking Active TSS	Brain Angular Gyrus	brain
23	chr1:46807000-46807600	Flanking Active TSS	Pancreas	Pancrea
24	chr1:46807000-46807600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:46807000-46807600	Flanking Active TSS	HMEC	breast
26	chr1:46807000-46807600	Flanking Active TSS	HUVEC	blood vessel
27	chr1:46807000-46807600	Flanking Active TSS	NH-A	brain
28	chr1:46807000-46807600	Flanking Active TSS	Osteobl	bone
29	chr1:46807000-46807800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:46807000-46807800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:46807000-46807800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:46807000-46807800	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr1:46807000-46807800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:46807000-46808000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:46807000-46808000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr1:46807000-46808800	Genic enhancers	Primary B cells from peripheral blood	blood
37	chr1:46807000-46810000	Enhancers	Fetal Heart	heart
38	chr1:46807000-46827200	Weak transcription	Fetal Brain Male	brain
39	chr1:46807200-46807600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:46807200-46807600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:46807200-46807600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:46807200-46807600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:46807200-46807600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:46807200-46807600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:46807200-46807600	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr1:46807200-46807600	Active TSS	Fetal Brain Female	brain
47	chr1:46807200-46807600	Enhancers	Fetal Lung	lung
48	chr1:46807200-46807600	Enhancers	Rectal Mucosa Donor 29	rectum
49	chr1:46807200-46807600	Enhancers	Right Atrium	heart
50	chr1:46807200-46807600	Enhancers	Sigmoid Colon	Sigmoid Colon

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