Variant report

Variant	rs28776801
Chromosome Location	chr4:73982294-73982295
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:73976291..73980439-chr4:73980496..73983422,3	K562	blood:
2	chr4:73981420..73983637-chr4:74123145..74125269,4	K562	blood:
3	chr4:73981590..73983818-chr4:73984797..73986757,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250220	Chromatin interaction
ENSG00000132466	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10028486	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11933644	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs16849102	0.85[EUR][1000 genomes]
rs16849106	0.85[EUR][1000 genomes]
rs16849108	0.85[EUR][1000 genomes]
rs16849146	0.81[ASN][1000 genomes]
rs16849150	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16849151	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16849172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16849185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2061574	0.85[EUR][1000 genomes]
rs2061575	0.85[EUR][1000 genomes]
rs2061577	0.85[EUR][1000 genomes]
rs2306057	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs2366716	0.85[EUR][1000 genomes]
rs28373296	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28460851	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28709646	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	0.91[ASN][1000 genomes]
rs4019514	0.85[EUR][1000 genomes]
rs4615148	0.81[EUR][1000 genomes]
rs4631009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4694589	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56235322	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56382488	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61149200	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61468561	0.81[EUR][1000 genomes]
rs67995155	0.96[EUR][1000 genomes]
rs6824334	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6845845	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]
rs6849701	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6851670	0.85[EUR][1000 genomes]
rs72859248	0.85[EUR][1000 genomes]
rs72859249	0.85[EUR][1000 genomes]
rs72861861	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7661799	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670286	0.81[EUR][1000 genomes]
rs7674847	0.85[EUR][1000 genomes]
rs7675007	0.85[EUR][1000 genomes]
rs7675027	0.84[EUR][1000 genomes]
rs7676278	0.85[EUR][1000 genomes]
rs7679277	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs7687433	0.85[EUR][1000 genomes]
rs7690799	0.84[EUR][1000 genomes]
rs7691344	0.80[EUR][1000 genomes]
rs7692425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[ASN][1000 genomes]
rs7692749	0.80[EUR][1000 genomes]
rs7694505	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	nsv1000509	chr4:73968978-74206949	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28776801	C4orf7	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73938800-74005200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:73939000-74005000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:73940400-74043400	Strong transcription	Fetal Thymus	thymus
4	chr4:73949200-73988200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr4:73950600-74004200	Strong transcription	HSMM	muscle
6	chr4:73952800-73992400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:73952800-74023000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:73954600-73992200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:73954600-73995400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr4:73955200-73991400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:73955200-73991600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:73955800-74019000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr4:73955800-74022400	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr4:73956000-73995600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:73957600-73985200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:73957800-73984200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:73964600-73985200	Weak transcription	Fetal Heart	heart
18	chr4:73966000-74005200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:73966000-74016800	Weak transcription	Psoas Muscle	Psoas
20	chr4:73966200-73989200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:73966600-73989800	Weak transcription	Colonic Mucosa	Colon
22	chr4:73967200-73984200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:73968000-73983600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:73968000-73983800	Weak transcription	Pancreas	Pancrea
25	chr4:73968000-73984400	Weak transcription	Spleen	Spleen
26	chr4:73968000-74005200	Weak transcription	Esophagus	oesophagus
27	chr4:73969200-74030200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr4:73969600-73994000	Strong transcription	Osteobl	bone
29	chr4:73969600-74020000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr4:73969800-73992800	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:73970200-73992400	Strong transcription	Fetal Intestine Large	intestine
32	chr4:73970200-74005000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr4:73970200-74005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:73970200-74005200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr4:73970600-73992400	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr4:73970800-74005200	Weak transcription	Small Intestine	intestine
37	chr4:73970800-74040800	Weak transcription	Stomach Mucosa	stomach
38	chr4:73971000-73994200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:73971200-74020000	Strong transcription	Dnd41	blood
40	chr4:73971400-73987400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:73971600-73992200	Strong transcription	Duodenum Mucosa	Duodenum
42	chr4:73971600-73993400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr4:73971600-74005200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr4:73971800-73985200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr4:73971800-73992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:73971800-74022600	Strong transcription	Liver	Liver
47	chr4:73971800-74032200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr4:73972200-73991000	Strong transcription	Primary B cells from cord blood	blood
49	chr4:73972600-73982400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr4:73972600-73983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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