Variant report

Variant	rs28709646
Chromosome Location	chr4:73945372-73945373
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:73941381..73942945-chr4:73944463..73946104,2	K562	blood:
2	chr4:73933733..73940261-chr4:73944971..73951272,10	K562	blood:
3	chr4:73934427..73936298-chr4:73944680..73946354,2	MCF-7	breast:
4	chr4:73944396..73945924-chr4:74118345..74120655,2	K562	blood:

Variant related genes	Relation type
ENSG00000163626	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10011483	0.83[YRI][hapmap]
rs10019296	0.83[YRI][hapmap]
rs10028486	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11933644	0.89[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.80[YRI][hapmap];0.87[ASN][1000 genomes]
rs16849102	0.90[ASN][1000 genomes]
rs16849106	0.93[ASN][1000 genomes]
rs16849108	0.93[ASN][1000 genomes]
rs16849146	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16849150	0.96[ASN][1000 genomes]
rs16849151	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs16849172	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16849185	0.89[ASW][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs2061574	0.93[ASN][1000 genomes]
rs2061575	0.93[ASN][1000 genomes]
rs2061576	0.90[ASN][1000 genomes]
rs2061577	0.93[ASN][1000 genomes]
rs2306057	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366716	0.90[ASN][1000 genomes]
rs28373296	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28460851	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28776801	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796680	0.88[ASN][1000 genomes]
rs4019514	0.90[ASN][1000 genomes]
rs4615148	0.82[ASN][1000 genomes]
rs4631009	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694589	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56235322	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56382488	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57330350	0.93[ASN][1000 genomes]
rs61149200	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61468561	0.90[ASN][1000 genomes]
rs61661011	0.87[ASN][1000 genomes]
rs6824334	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs6845845	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]
rs6848243	1.00[CEU][hapmap]
rs6849701	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851670	0.93[ASN][1000 genomes]
rs72663032	0.83[ASN][1000 genomes]
rs72859248	0.90[ASN][1000 genomes]
rs72859249	0.90[ASN][1000 genomes]
rs72861861	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7661799	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7664144	0.85[LWK][hapmap];0.83[YRI][hapmap]
rs7670286	0.90[ASN][1000 genomes]
rs7674847	0.90[ASN][1000 genomes]
rs7675007	0.91[ASN][1000 genomes]
rs7675027	0.91[ASN][1000 genomes]
rs7676278	0.90[ASN][1000 genomes]
rs7679277	0.89[ASW][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7687433	0.90[ASN][1000 genomes]
rs7690799	0.90[ASN][1000 genomes]
rs7691344	0.90[ASN][1000 genomes]
rs7692425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7692749	0.90[ASN][1000 genomes]
rs7694505	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[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
rs28709646	ANKRD56	cis	cerebellum	SCAN
rs28709646	C4orf7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73936000-73956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:73936000-73956400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:73936000-73956400	Weak transcription	Aorta	Aorta
4	chr4:73936000-73956400	Weak transcription	Esophagus	oesophagus
5	chr4:73936000-73956400	Weak transcription	Gastric	stomach
6	chr4:73936000-73956400	Weak transcription	Pancreas	Pancrea
7	chr4:73936000-73956800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:73936000-73969600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:73936200-73946000	Weak transcription	Fetal Heart	heart
10	chr4:73936200-73950000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr4:73936200-73951800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:73936200-73956400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:73936200-73956600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr4:73936200-73980000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:73936400-73951800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:73936400-73952000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr4:73936400-73970000	Weak transcription	Stomach Mucosa	stomach
18	chr4:73937200-73946000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:73937400-73945600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:73937600-73945400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr4:73937600-73951400	Strong transcription	Placenta	Placenta
22	chr4:73937800-73946400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:73938000-73945600	Strong transcription	GM12878-XiMat	blood
24	chr4:73938400-73949000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:73938600-73946600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr4:73938600-73946600	Strong transcription	Liver	Liver
27	chr4:73938600-73951200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr4:73938600-73953600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:73938800-73945600	Strong transcription	Osteobl	bone
30	chr4:73938800-73954800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:73938800-74005200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr4:73939000-73969600	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:73939000-74005000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:73939200-73945600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:73939200-73950000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr4:73939200-73951200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:73939200-73951200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:73939400-73953000	Strong transcription	Dnd41	blood
39	chr4:73939400-73955200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr4:73939400-73970000	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:73940400-73950800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr4:73940400-73951200	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr4:73940400-74043400	Strong transcription	Fetal Thymus	thymus
44	chr4:73940600-73946000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr4:73940600-73947000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:73940600-73947200	Strong transcription	Duodenum Mucosa	Duodenum
47	chr4:73940600-73950000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:73940600-73950800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr4:73940600-73951200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr4:73940600-73951200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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