Variant report

Variant	rs3733448
Chromosome Location	chr4:90036463-90036464
allele	C/T
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	POLR2A	chr4:90032368-90036875	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:90035789-90036849	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr4:90032629-90036890	K562	blood:	n/a	n/a
4	POLR2A	chr4:90031723-90036966	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:90032004..90034943-chr4:90035415..90038647,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270720	TF binding region
FAM13A	TF binding region
ENSG00000180346	Chromatin interaction
ENSG00000138640	Chromatin interaction
ENSG00000271359	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10433948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433949	1.00[ASW][hapmap];0.88[CEU][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10470936	0.82[JPT][hapmap]
rs11097216	0.88[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11725475	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11725938	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11726708	0.86[CEU][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730277	0.96[AMR][1000 genomes];0.81[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	0.81[EUR][1000 genomes]
rs12505696	0.88[JPT][hapmap]
rs12507131	0.88[CEU][hapmap];0.88[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508524	0.83[ASW][hapmap];0.88[JPT][hapmap]
rs12509305	0.88[JPT][hapmap]
rs12647781	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1398942	0.88[JPT][hapmap]
rs1533292	0.83[ASN][1000 genomes]
rs1533293	0.88[CEU][hapmap];0.88[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4367140	0.84[ASN][1000 genomes]
rs56943497	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57987710	0.81[AMR][1000 genomes]
rs58377799	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58633349	0.85[AMR][1000 genomes]
rs59684168	0.83[AFR][1000 genomes];0.91[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];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61138976	0.85[AMR][1000 genomes]
rs61315828	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66475381	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66500341	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[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];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67412466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67706608	0.85[ASN][1000 genomes]
rs67850063	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6817766	0.88[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6838424	0.82[JPT][hapmap]
rs72613157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9994655	0.88[CEU][hapmap];0.88[JPT][hapmap];0.85[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:59 , 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	chr4:90033800-90037600	Weak transcription	Fetal Thymus	thymus
13	chr4:90033800-90037600	Weak transcription	HSMM	muscle
14	chr4:90033800-90042400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:90034000-90037000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:90034000-90037000	Weak transcription	Fetal Lung	lung
17	chr4:90034000-90038400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:90034000-90038800	Weak transcription	Fetal Kidney	kidney
19	chr4:90034000-90039000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:90034000-90040400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr4:90034000-90040400	Weak transcription	NH-A	brain
22	chr4:90034000-90040800	Weak transcription	Osteobl	bone
23	chr4:90034000-90041600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:90034000-90042400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr4:90034000-90044000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr4:90034200-90038400	Weak transcription	Fetal Brain Male	brain
27	chr4:90034200-90040600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr4:90034200-90040800	Weak transcription	NHDF-Ad	bronchial
29	chr4:90034200-90041000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr4:90034200-90044000	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:90034400-90036600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:90034400-90039000	Weak transcription	Dnd41	blood
33	chr4:90034400-90043000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:90034400-90044000	Weak transcription	Brain Substantia Nigra	brain
35	chr4:90034600-90037000	ZNF genes & repeats	Primary T cells from cord blood	blood
36	chr4:90034600-90040400	Weak transcription	HMEC	breast
37	chr4:90034600-90041600	Weak transcription	Fetal Intestine Large	intestine
38	chr4:90034600-90042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr4:90034800-90039200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr4:90034800-90040400	Weak transcription	NHEK	skin
41	chr4:90034800-90049200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:90035000-90037600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:90035000-90043600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:90035200-90042600	Weak transcription	Fetal Intestine Small	intestine
45	chr4:90035200-90042600	Weak transcription	K562	blood
46	chr4:90035400-90037200	Weak transcription	A549	lung
47	chr4:90035400-90038800	Enhancers	Liver	Liver
48	chr4:90035400-90044600	Weak transcription	Fetal Muscle Leg	muscle
49	chr4:90035600-90037000	Enhancers	HepG2	liver
50	chr4:90035600-90039600	Weak transcription	Fetal Stomach	stomach

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