Variant report

Variant	rs3744822
Chromosome Location	chr18:9258537-9258538
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	POLR2A	chr18:9258498-9258575	HepG2	liver:	n/a	n/a
2	POLR2A	chr18:9256013-9259094	K562	blood:	n/a	n/a
3	POLR2A	chr18:9256925-9259546	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr18:9257452..9259305-chr18:9285325..9287150,2	K562	blood:
2	chr18:9249091..9251466-chr18:9256573..9259954,3	K562	blood:
3	chr18:9252289..9254016-chr18:9256022..9258799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273284	TF binding region
ENSG00000207092	Chromatin interaction
ENSG00000200883	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1046483	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10502391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1114591	0.93[ASN][1000 genomes]
rs11659948	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12326829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443598	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16954914	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17413344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs17497377	1.00[GIH][hapmap]
rs17498752	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17498969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17499116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2120316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2377962	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs28520663	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28578690	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28619483	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28637808	0.93[ASN][1000 genomes]
rs2864515	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28820062	0.86[ASN][1000 genomes]
rs28844999	0.86[ASN][1000 genomes]
rs3213925	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4356535	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4449017	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4490062	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5011606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56996721	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57567668	0.93[ASN][1000 genomes]
rs58350342	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59018067	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59616258	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59633812	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59864974	0.93[ASN][1000 genomes]
rs59983698	0.80[EUR][1000 genomes]
rs60119987	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60143204	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60354371	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62085951	0.93[ASN][1000 genomes]
rs6506651	0.86[ASN][1000 genomes]
rs7229105	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7234017	0.86[ASN][1000 genomes]
rs7235358	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7237039	0.86[ASN][1000 genomes]
rs7242002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7242624	0.86[ASN][1000 genomes]
rs72935233	0.80[EUR][1000 genomes]
rs72935236	0.80[EUR][1000 genomes]
rs72935248	0.82[EUR][1000 genomes]
rs72935249	0.82[EUR][1000 genomes]
rs72935251	0.82[EUR][1000 genomes]
rs72935253	0.82[EUR][1000 genomes]
rs72935258	0.82[EUR][1000 genomes]
rs72935260	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72935263	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72935265	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72935266	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72935267	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72935274	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72937244	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72937245	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72937248	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72937250	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72937257	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72937258	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937259	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937267	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937287	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937291	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937297	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937301	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72937302	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939207	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939211	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939216	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939219	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939220	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939221	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939224	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939230	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939232	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939235	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939239	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7505782	0.83[AMR][1000 genomes]
rs7506375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7506561	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8089057	0.86[ASN][1000 genomes]
rs8094979	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8096630	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8098516	0.86[ASN][1000 genomes]
rs8098544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099583	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9652921	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9675513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes]
rs9748482	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9748485	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9748751	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv431971	chr18:9081185-9326852	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1055696	chr18:9191679-9309805	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv458023	chr18:9240413-9357786	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv576447	chr18:9240413-9357786	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv2201	chr18:9247631-9279825	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9192200-9284000	Weak transcription	NHEK	skin
2	chr18:9216000-9289600	Weak transcription	HMEC	breast
3	chr18:9232600-9261400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr18:9232800-9273000	Weak transcription	Fetal Kidney	kidney
5	chr18:9233200-9264200	Weak transcription	Brain Anterior Caudate	brain
6	chr18:9233400-9265800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr18:9234200-9264200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr18:9234400-9280400	Weak transcription	Psoas Muscle	Psoas
9	chr18:9234600-9264800	Weak transcription	Colonic Mucosa	Colon
10	chr18:9234600-9278000	Weak transcription	Brain Angular Gyrus	brain
11	chr18:9234800-9264200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr18:9234800-9264800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr18:9234800-9264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr18:9234800-9264800	Weak transcription	Lung	lung
15	chr18:9234800-9264800	Weak transcription	Pancreas	Pancrea
16	chr18:9234800-9290000	Weak transcription	NHLF	lung
17	chr18:9235000-9264600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr18:9235000-9264800	Weak transcription	Gastric	stomach
19	chr18:9235000-9264800	Weak transcription	Right Ventricle	heart
20	chr18:9235000-9285400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr18:9235200-9260800	Weak transcription	Esophagus	oesophagus
22	chr18:9235200-9264200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr18:9235200-9264600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr18:9235400-9264800	Weak transcription	Fetal Stomach	stomach
25	chr18:9235400-9270800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr18:9235600-9264600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr18:9235800-9260800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr18:9235800-9264800	Weak transcription	Thymus	Thymus
29	chr18:9236600-9264200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr18:9237000-9264200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr18:9239600-9264600	Weak transcription	HepG2	liver
32	chr18:9240400-9264800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:9240600-9275800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr18:9240800-9279800	Weak transcription	Colon Smooth Muscle	Colon
35	chr18:9241000-9260400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr18:9242800-9264800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr18:9243600-9278000	Weak transcription	Brain Cingulate Gyrus	brain
38	chr18:9243600-9283000	Weak transcription	Brain Substantia Nigra	brain
39	chr18:9244200-9264800	Weak transcription	Brain Hippocampus Middle	brain
40	chr18:9244800-9260800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr18:9245000-9271000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr18:9245600-9264200	Weak transcription	Osteobl	bone
43	chr18:9247800-9258800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr18:9249000-9264800	Weak transcription	Aorta	Aorta
45	chr18:9252200-9259200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr18:9252200-9259800	Strong transcription	Placenta	Placenta
47	chr18:9252400-9264800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:9252400-9265000	Strong transcription	HSMM	muscle
49	chr18:9252800-9264400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr18:9254200-9261800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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