Variant report

Variant	rs9311440
Chromosome Location	chr3:49331864-49331865
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	chr3:49331820-49332270	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:49331720-49332158	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr3:49331830-49332054	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr3:49331797-49332154	HUVEC	blood vessel:	n/a	n/a
5	GATA2	chr3:49331729-49332086	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
USP4	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10049462	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs11719220	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs13068038	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs13077498	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs13321689	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs28690891	1.00[AMR][1000 genomes]
rs35060561	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9818758	0.89[YRI][hapmap]
rs9828212	1.00[AMR][1000 genomes]
rs9839368	1.00[ASW][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes]
rs9844757	1.00[ASW][hapmap];0.89[YRI][hapmap]
rs9858407	1.00[AMR][1000 genomes]
rs9873994	0.89[YRI][hapmap]
rs9880088	1.00[ASW][hapmap];0.89[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49349400	Strong transcription	Dnd41	blood
3	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:49314800-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
9	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
12	chr3:49315400-49335800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
14	chr3:49315600-49332400	Strong transcription	Brain Hippocampus Middle	brain
15	chr3:49315800-49333000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:49315800-49349200	Strong transcription	Fetal Brain Female	brain
17	chr3:49316200-49334600	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:49316600-49340200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:49317200-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:49317200-49349400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
23	chr3:49317400-49332200	Strong transcription	Right Ventricle	heart
24	chr3:49317400-49334200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:49317400-49334200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:49317400-49334200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:49317400-49334200	Strong transcription	Fetal Muscle Leg	muscle
28	chr3:49317400-49334200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:49317400-49334600	Strong transcription	Left Ventricle	heart
30	chr3:49317400-49349200	Strong transcription	Fetal Intestine Large	intestine
31	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:49319200-49333600	Strong transcription	HSMMtube	muscle
35	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:49319400-49333000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr3:49319400-49349600	Strong transcription	Liver	Liver
38	chr3:49319600-49332600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:49319600-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:49319600-49344000	Strong transcription	Osteobl	bone
41	chr3:49319600-49349400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:49319800-49349200	Strong transcription	Brain Germinal Matrix	brain
44	chr3:49319800-49349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:49320000-49332400	Strong transcription	Rectal Smooth Muscle	rectum
46	chr3:49320000-49337600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:49320000-49340600	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr3:49320000-49349000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:49320000-49349600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr3:49320200-49375000	Strong transcription	Thymus	Thymus

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