Variant report

Variant	rs5020219
Chromosome Location	chr4:74036166-74036167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:74030620..74034303-chr4:74034423..74038254,3	MCF-7	breast:
2	chr4:73933887..73935834-chr4:74035566..74037820,2	MCF-7	breast:
3	chr4:74029391..74031667-chr4:74035341..74038120,3	K562	blood:
4	chr4:74030522..74032070-chr4:74034879..74036523,2	MCF-7	breast:
5	chr4:74028581..74032881-chr4:74033688..74038120,5	K562	blood:

Variant related genes	Relation type
ENSG00000163626	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10006547	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10034689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10035001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10050235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10805059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11724514	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs11736349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap]
rs11935070	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs13101277	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1534450	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4072	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs4437217	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694155	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4694156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4995246	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[EUR][1000 genomes]
rs6830954	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6850870	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9291182	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][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	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	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
8	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
9	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
10	nsv879486	chr4:74031423-74114322	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:73940400-74043400	Strong transcription	Fetal Thymus	thymus
2	chr4:73970800-74040800	Weak transcription	Stomach Mucosa	stomach
3	chr4:74006800-74043400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:74008000-74039000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr4:74008800-74059600	Weak transcription	Fetal Brain Male	brain
6	chr4:74014600-74046400	Weak transcription	Hela-S3	cervix
7	chr4:74018400-74055200	Weak transcription	Psoas Muscle	Psoas
8	chr4:74019200-74043400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:74024200-74043200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:74025600-74040800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr4:74027800-74043600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:74028200-74037000	Weak transcription	Fetal Heart	heart
13	chr4:74028800-74037200	Strong transcription	Osteobl	bone
14	chr4:74030600-74039600	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr4:74030800-74037400	Strong transcription	Primary B cells from cord blood	blood
16	chr4:74030800-74043000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:74030800-74043400	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr4:74031000-74036800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:74031000-74037200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:74031000-74037600	Strong transcription	Liver	Liver
21	chr4:74031000-74039400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr4:74031000-74039400	Strong transcription	HSMM	muscle
23	chr4:74031000-74043600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:74031000-74043800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr4:74031200-74037000	Strong transcription	Adipose Nuclei	Adipose
26	chr4:74031400-74037000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr4:74031400-74037200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr4:74031400-74037800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr4:74031400-74041800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr4:74031600-74036800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
31	chr4:74031600-74043400	ZNF genes & repeats	GM12878-XiMat	blood
32	chr4:74031600-74066800	Weak transcription	HMEC	breast
33	chr4:74031600-74077200	Weak transcription	Small Intestine	intestine
34	chr4:74031800-74038200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr4:74032200-74036800	Strong transcription	HUVEC	blood vessel
36	chr4:74032200-74037000	Strong transcription	Fetal Brain Female	brain
37	chr4:74032200-74039400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr4:74032400-74037000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr4:74032400-74039600	Strong transcription	HepG2	liver
40	chr4:74032400-74039800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr4:74032400-74042800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:74032600-74037400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr4:74032600-74037600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:74032600-74037600	Strong transcription	Fetal Lung	lung
45	chr4:74032600-74038800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:74032800-74037800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr4:74032800-74038400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr4:74033000-74036600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:74033000-74037800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr4:74033000-74038000	Strong transcription	Fetal Muscle Trunk	muscle

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