Variant report

Variant	rs6845845
Chromosome Location	chr4:73937533-73937534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:73933987-73938824	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:73933774-73940652	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr4:73932730..73938383-chr4:74120374..74126369,19	MCF-7	breast:
2	chr4:73932413..73938405-chr4:74120693..74126649,20	K562	blood:
3	chr4:73933853..73938156-chr4:74122325..74126609,11	MCF-7	breast:
4	chr4:73933733..73940261-chr4:73944971..73951272,10	K562	blood:
5	chr4:73935991..73938243-chr4:73939866..73943028,3	MCF-7	breast:
6	chr4:73937231..73939803-chr4:73989844..73991440,2	MCF-7	breast:
7	chr4:73936677..73938384-chr4:73949086..73951133,2	K562	blood:
8	chr4:73935697..73938627-chr4:73959449..73961748,2	K562	blood:
9	chr4:73929823..73938112-chr4:74120693..74129342,27	K562	blood:

No data

Variant related genes	Relation type
COX18	TF binding region
ENSG00000132466	Chromatin interaction
ENSG00000250220	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10028486	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs11933644	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[ASN][1000 genomes]
rs16849102	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16849106	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16849108	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16849146	0.96[ASN][1000 genomes]
rs16849150	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16849151	1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16849172	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16849185	0.94[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2061574	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2061575	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2061576	0.90[ASN][1000 genomes]
rs2061577	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2306057	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366716	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28373296	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28460851	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28709646	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28776801	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796680	0.88[ASN][1000 genomes]
rs4019514	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4615148	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4631009	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694589	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56235322	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56382488	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57330350	0.93[ASN][1000 genomes]
rs61149200	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61468561	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61661011	0.87[ASN][1000 genomes]
rs67995155	0.91[EUR][1000 genomes]
rs6824334	0.94[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs6849701	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851670	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72663032	0.83[ASN][1000 genomes]
rs72859248	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72859249	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72861861	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661799	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7670286	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7674847	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7675007	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675027	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7676278	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679277	0.94[CEU][hapmap];0.80[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[ASN][1000 genomes]
rs7687433	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7690799	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7691344	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7692425	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7692749	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7694505	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949371	chr4:73678470-74094500	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv432611	chr4:73740665-74099265	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv523169	chr4:73752242-74120910	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv998707	chr4:73753922-74044843	Weak transcription Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv537136	chr4:73753922-74044843	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv917017	chr4:73754127-74044830	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv1013174	chr4:73785324-74031884	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv537137	chr4:73785324-74031884	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1012068	chr4:73817769-74003079	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv1014088	chr4:73817769-74031884	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv537138	chr4:73817769-74031884	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv533502	chr4:73819067-74044813	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	esv1849323	chr4:73926670-74115116	Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6845845	ANKRD56	cis	cerebellum	SCAN
rs6845845	C4orf7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73935600-73943600	Weak transcription	Spleen	Spleen
2	chr4:73935800-73941600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:73935800-73942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:73935800-73942400	Weak transcription	Small Intestine	intestine
5	chr4:73935800-73943600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr4:73936000-73938800	Weak transcription	Hela-S3	cervix
7	chr4:73936000-73940400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:73936000-73940600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:73936000-73941000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:73936000-73941600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:73936000-73941600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr4:73936000-73941600	Weak transcription	Left Ventricle	heart
13	chr4:73936000-73941800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr4:73936000-73941800	Weak transcription	Ovary	ovary
15	chr4:73936000-73942600	Weak transcription	Lung	lung
16	chr4:73936000-73956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:73936000-73956400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:73936000-73956400	Weak transcription	Aorta	Aorta
19	chr4:73936000-73956400	Weak transcription	Esophagus	oesophagus
20	chr4:73936000-73956400	Weak transcription	Gastric	stomach
21	chr4:73936000-73956400	Weak transcription	Pancreas	Pancrea
22	chr4:73936000-73956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:73936000-73969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr4:73936200-73937600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:73936200-73937600	Weak transcription	Placenta	Placenta
26	chr4:73936200-73937800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr4:73936200-73938000	Weak transcription	GM12878-XiMat	blood
28	chr4:73936200-73938400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:73936200-73938600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr4:73936200-73938600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:73936200-73938600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr4:73936200-73938600	Weak transcription	Liver	Liver
33	chr4:73936200-73938600	Weak transcription	HSMM	muscle
34	chr4:73936200-73938800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:73936200-73938800	Weak transcription	HMEC	breast
36	chr4:73936200-73938800	Weak transcription	NHDF-Ad	bronchial
37	chr4:73936200-73939000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr4:73936200-73939200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:73936200-73939200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr4:73936200-73939200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr4:73936200-73939400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr4:73936200-73939400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr4:73936200-73939600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:73936200-73939600	Weak transcription	HUVEC	blood vessel
45	chr4:73936200-73940000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr4:73936200-73940400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr4:73936200-73940400	Weak transcription	Fetal Thymus	thymus
48	chr4:73936200-73940400	Weak transcription	NHLF	lung
49	chr4:73936200-73940600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:73936200-73940600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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