Variant report

Variant	rs10433948
Chromosome Location	chr4:90037951-90037952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZC3H11A	chr4:90037927-90038018	K562	blood:	n/a	n/a
2	POLR2A	chr4:90037397-90038363	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:90037701-90038146	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:90037746-90038323	K562	blood:	n/a	n/a
5	POLR2A	chr4:90037700-90038151	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:90036870..90039187-chr4:90043124..90046686,3	MCF-7	breast:
2	chr4:90036910..90039747-chr4:90043122..90045290,2	MCF-7	breast:
3	chr4:90037816..90038427-chrX:121120534..121121165,2	MCF-7	breast:
4	chr4:90036580..90038226-chr4:90055929..90057591,2	K562	blood:
5	chr4:90032004..90034943-chr4:90035415..90038647,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270720	TF binding region
ENSG00000138640	Chromatin interaction
ENSG00000180346	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10433949	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097216	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11725475	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11725938	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730277	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502070	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12505523	0.84[EUR][1000 genomes]
rs12507131	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647781	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1533292	0.83[ASN][1000 genomes]
rs1533293	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3733448	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4367140	0.84[ASN][1000 genomes]
rs56943497	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57987710	0.81[AMR][1000 genomes]
rs58377799	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58633349	0.85[AMR][1000 genomes]
rs59684168	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59710447	0.81[AMR][1000 genomes]
rs59799062	0.83[ASN][1000 genomes]
rs60770708	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61138976	0.85[AMR][1000 genomes]
rs61315828	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66475381	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66500341	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66869930	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs67287708	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67412466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67706608	0.85[ASN][1000 genomes]
rs67850063	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6817766	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72613157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72877639	0.84[ASN][1000 genomes]
rs72877679	0.85[AMR][1000 genomes]
rs72877685	0.85[AMR][1000 genomes]
rs9790655	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9994655	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470051	chr4:89644931-90643144	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1007025	chr4:89837734-90098046	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537176	chr4:89837734-90098046	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1002448	chr4:89933385-90128133	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:90033400-90048200	Weak transcription	Ovary	ovary
2	chr4:90033400-90049200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:90033600-90038400	Weak transcription	Psoas Muscle	Psoas
4	chr4:90033600-90039000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:90033600-90039000	Weak transcription	Lung	lung
6	chr4:90033600-90040800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr4:90033600-90043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:90033600-90045600	Weak transcription	Esophagus	oesophagus
9	chr4:90033600-90045600	Weak transcription	Pancreas	Pancrea
10	chr4:90033600-90049200	Weak transcription	Gastric	stomach
11	chr4:90033600-90052200	Weak transcription	Aorta	Aorta
12	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:90034000-90038400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr4:90034000-90038800	Weak transcription	Fetal Kidney	kidney
15	chr4:90034000-90039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr4:90034000-90040400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:90034000-90040400	Weak transcription	NH-A	brain
18	chr4:90034000-90040800	Weak transcription	Osteobl	bone
19	chr4:90034000-90041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:90034200-90038400	Weak transcription	Fetal Brain Male	brain
23	chr4:90034200-90040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:90034200-90040800	Weak transcription	NHDF-Ad	bronchial
25	chr4:90034200-90041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:90034400-90039000	Weak transcription	Dnd41	blood
28	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
30	chr4:90034600-90040400	Weak transcription	HMEC	breast
31	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
32	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:90034800-90039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr4:90034800-90040400	Weak transcription	NHEK	skin
35	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
38	chr4:90035200-90042600	Weak transcription	K562	blood
39	chr4:90035400-90038800	Enhancers	Liver	Liver
40	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
41	chr4:90035600-90039600	Weak transcription	Fetal Stomach	stomach
42	chr4:90035600-90040800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:90035600-90041000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:90035600-90041000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr4:90035600-90041800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:90035600-90043600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:90035600-90044000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:90036200-90041000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:90036600-90044800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:90037000-90046200	Weak transcription	Primary T cells from cord blood	blood

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