Variant report

Variant	rs2036616
Chromosome Location	chr3:43340352-43340353
allele	A/C
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	chr3:43339445-43340689	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:43338696..43340515-chr3:43344515..43347425,2	K562	blood:
2	chr3:43338773..43340383-chr3:43342318..43344854,2	K562	blood:
3	chr3:43327770..43329938-chr3:43337733..43342180,4	K562	blood:
4	chr3:43289737..43291817-chr3:43339501..43341574,2	K562	blood:

Variant related genes	Relation type
SNRK	TF binding region
ENSG00000163788	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10084663	0.87[AFR][1000 genomes]
rs11129997	1.00[AFR][1000 genomes]
rs11129998	1.00[AFR][1000 genomes]
rs11130003	0.90[YRI][hapmap];0.94[AFR][1000 genomes]
rs1120779	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11713302	0.94[AFR][1000 genomes]
rs12495394	0.88[AFR][1000 genomes]
rs12497714	0.82[AFR][1000 genomes]
rs12632805	0.90[YRI][hapmap]
rs1320159	0.83[AFR][1000 genomes]
rs1395373	1.00[MEX][hapmap];0.94[MKK][hapmap]
rs1472807	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1506618	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1996496	0.85[AFR][1000 genomes]
rs2135510	0.88[AFR][1000 genomes]
rs2372357	0.83[AFR][1000 genomes]
rs2372358	0.83[AFR][1000 genomes]
rs2372359	0.85[AFR][1000 genomes]
rs2372373	1.00[AMR][1000 genomes]
rs2888311	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4234427	0.81[AFR][1000 genomes]
rs4234466	0.83[AFR][1000 genomes]
rs4339089	0.88[AFR][1000 genomes]
rs4346523	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4405884	0.83[AFR][1000 genomes]
rs4420837	0.82[AFR][1000 genomes]
rs4425230	0.83[AFR][1000 genomes]
rs4470482	0.83[AFR][1000 genomes]
rs4569634	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4642093	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4682673	0.83[AFR][1000 genomes]
rs4682674	0.83[AFR][1000 genomes]
rs4682681	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs4682684	0.94[AFR][1000 genomes]
rs4682688	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs4682881	1.00[AMR][1000 genomes]
rs4682884	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs4683365	0.90[YRI][hapmap]
rs6441771	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6442145	0.83[AFR][1000 genomes]
rs6766825	0.85[AFR][1000 genomes]
rs6767741	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs6775392	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6784075	0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs6791682	0.83[AFR][1000 genomes]
rs6793755	0.97[AFR][1000 genomes]
rs7616072	1.00[AFR][1000 genomes]
rs7632743	1.00[ASW][hapmap]
rs7636644	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7647197	0.82[AFR][1000 genomes]
rs7648023	0.91[AFR][1000 genomes]
rs7651008	1.00[AMR][1000 genomes]
rs7651091	0.85[AFR][1000 genomes]
rs906156	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs906157	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs906158	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs937827	1.00[ASW][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes]
rs9755005	0.97[AFR][1000 genomes]
rs984345	0.94[AFR][1000 genomes]
rs9846341	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9859465	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752008	chr3:43285369-43360879	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1009102	chr3:43285369-43369712	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv876732	chr3:43326887-43360879	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43329200-43344800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:43329200-43346800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:43329400-43346400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:43329600-43345000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:43330400-43344800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:43330800-43344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr3:43330800-43359000	Weak transcription	Fetal Brain Male	brain
8	chr3:43331000-43340600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:43331000-43344600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:43331200-43344600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:43331400-43344600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr3:43331400-43344600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:43331400-43358200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:43331600-43344600	Weak transcription	Placenta	Placenta
15	chr3:43331600-43344600	Weak transcription	Hela-S3	cervix
16	chr3:43331600-43344800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:43332400-43361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:43332800-43377000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:43333000-43344600	Weak transcription	Fetal Brain Female	brain
20	chr3:43333000-43344600	Weak transcription	NH-A	brain
21	chr3:43333200-43344800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:43334400-43340600	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:43334800-43342200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:43335000-43344600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:43335400-43344600	Weak transcription	Ovary	ovary
26	chr3:43335400-43351000	Weak transcription	Fetal Stomach	stomach
27	chr3:43336800-43344600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:43337000-43344600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:43337000-43344800	Weak transcription	Fetal Kidney	kidney
30	chr3:43337000-43354400	Weak transcription	A549	lung
31	chr3:43337400-43340600	Enhancers	Adipose Nuclei	Adipose
32	chr3:43337400-43358200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:43338000-43341200	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr3:43338200-43342400	Weak transcription	Fetal Intestine Small	intestine
35	chr3:43338400-43342600	Genic enhancers	HUVEC	blood vessel
36	chr3:43338400-43344600	Weak transcription	Fetal Lung	lung
37	chr3:43338400-43344600	Weak transcription	NHDF-Ad	bronchial
38	chr3:43338600-43340800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:43338600-43341000	Enhancers	Primary B cells from peripheral blood	blood
40	chr3:43338600-43344000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:43338600-43344000	Weak transcription	Fetal Intestine Large	intestine
42	chr3:43338600-43344600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:43338600-43344600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:43338600-43344600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:43338600-43344600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:43338600-43344600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:43338600-43344600	Weak transcription	HSMM	muscle
48	chr3:43338600-43344800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:43338600-43344800	Weak transcription	HSMMtube	muscle
50	chr3:43338600-43344800	Weak transcription	K562	blood

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