Variant report

Variant	rs3823859
Chromosome Location	chr7:120483336-120483337
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:120476774..120479662-chr7:120483201..120485392,2	K562	blood:
2	chr7:120475241..120477501-chr7:120481801..120483425,2	MCF-7	breast:
3	chr7:120483102..120485878-chr7:120487827..120490041,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106025	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10225453	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10252911	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs10257297	0.80[ASN][1000 genomes]
rs10257475	0.80[ASN][1000 genomes]
rs10266755	0.82[ASW][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10272601	0.81[JPT][hapmap]
rs10274689	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279837	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953922	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10953923	0.80[ASW][hapmap]
rs11982493	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12669167	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13231854	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1557857	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17142976	0.85[CEU][hapmap]
rs17142995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17143001	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs17143009	0.85[CEU][hapmap];0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs1859316	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1859318	0.83[ASN][1000 genomes]
rs1859319	0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2040762	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058501	0.80[ASW][hapmap]
rs2074577	0.86[ASW][hapmap]
rs2097806	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs2107275	0.86[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2107276	0.90[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2244863	0.86[ASW][hapmap]
rs2248890	0.80[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2524949	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2524951	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2525705	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2525709	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2525743	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2721339	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2721341	0.93[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2721343	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2721347	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2721354	0.93[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap]
rs2721363	0.86[ASW][hapmap]
rs2721364	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3735467	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3757556	0.81[JPT][hapmap]
rs3757557	0.83[CHD][hapmap]
rs3779386	0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3779387	0.80[ASN][1000 genomes]
rs3814460	0.89[ASN][1000 genomes]
rs3823861	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.80[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4141309	0.83[CHD][hapmap]
rs41611	0.82[ASN][1000 genomes]
rs41621	0.87[ASN][1000 genomes]
rs41622	0.81[CEU][hapmap]
rs41624	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.87[ASN][1000 genomes]
rs41627	0.87[ASN][1000 genomes]
rs41628	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs41629	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs41632	0.95[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.80[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41690	0.86[ASW][hapmap]
rs4445165	0.89[ASN][1000 genomes]
rs55855220	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61452531	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6466759	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466760	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466761	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466762	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6944789	0.80[ASW][hapmap]
rs6953454	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958947	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6959328	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6964344	0.81[JPT][hapmap]
rs6964667	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964786	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6971854	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs6979247	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs714259	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73427805	0.89[ASN][1000 genomes]
rs73427862	0.81[ASN][1000 genomes]
rs73427866	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73429803	0.80[ASN][1000 genomes]
rs73721472	0.81[EUR][1000 genomes]
rs745167	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7776721	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs7781985	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7800318	0.87[ASN][1000 genomes]
rs7805211	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7805733	0.81[CEU][hapmap]
rs7810542	0.95[CEU][hapmap]
rs9649429	0.80[ASN][1000 genomes]
rs996903	0.93[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3823859	TSPAN12	cis	Esophagus Muscularis	GTEx
rs3823859	TSPAN12	cis	parietal	SCAN
rs3823859	TSPAN12	cis	Artery Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120443000-120488000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:120445200-120494400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr7:120468600-120487600	Weak transcription	Lung	lung
4	chr7:120470600-120484600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:120474000-120492400	Weak transcription	Fetal Lung	lung
6	chr7:120474000-120496400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr7:120474600-120496600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr7:120476400-120484200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:120476600-120492400	Weak transcription	Gastric	stomach
10	chr7:120477000-120489800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr7:120477000-120492400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:120477200-120496200	Weak transcription	Aorta	Aorta
13	chr7:120478000-120483400	Weak transcription	Fetal Stomach	stomach
14	chr7:120478000-120483400	Weak transcription	Left Ventricle	heart
15	chr7:120478400-120487400	Weak transcription	Colonic Mucosa	Colon
16	chr7:120479400-120484000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:120479400-120488000	Weak transcription	Right Atrium	heart
18	chr7:120479600-120494000	Weak transcription	HUVEC	blood vessel
19	chr7:120480000-120488000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:120480200-120485000	Weak transcription	Fetal Heart	heart
21	chr7:120482000-120484200	Genic enhancers	Fetal Kidney	kidney
22	chr7:120482200-120483400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr7:120482200-120483600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:120482200-120483600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:120482200-120483800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr7:120482200-120483800	Enhancers	Pancreas	Pancrea
27	chr7:120482400-120484600	Strong transcription	Fetal Intestine Large	intestine
28	chr7:120482400-120484600	Strong transcription	Fetal Muscle Leg	muscle
29	chr7:120482600-120483400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:120482600-120483400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr7:120482600-120495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:120482600-120496200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr7:120482800-120483400	Weak transcription	Fetal Intestine Small	intestine
34	chr7:120482800-120484000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr7:120482800-120484600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr7:120482800-120484800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr7:120482800-120485000	Weak transcription	Small Intestine	intestine
38	chr7:120482800-120487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr7:120482800-120492200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr7:120482800-120496400	Weak transcription	Liver	Liver
41	chr7:120482800-120496400	Weak transcription	Rectal Smooth Muscle	rectum
42	chr7:120482800-120496600	Weak transcription	Stomach Mucosa	stomach
43	chr7:120483000-120483400	Weak transcription	Colon Smooth Muscle	Colon
44	chr7:120483200-120483400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr7:120483200-120483400	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr7:120483200-120483600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:120483200-120483600	Enhancers	Placenta Amnion	Placenta Amnion
48	chr7:120483200-120483800	Enhancers	Right Ventricle	heart
49	chr7:120483200-120485400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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