Variant report

Variant	rs2241784
Chromosome Location	chr3:51418348-51418349
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	STAT3	chr3:51418190-51418436	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:51416005..51420526-chr3:51420969..51426466,5	MCF-7	breast:

Variant related genes	Relation type
MANF	TF binding region
ENSG00000145050	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1031925	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10433609	0.90[CHB][hapmap]
rs10865970	0.82[EUR][1000 genomes]
rs11130286	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs11130290	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs11706571	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs12632046	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1318649	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap]
rs1383251	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1480353	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1480354	0.82[EUR][1000 genomes]
rs1480360	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1480362	0.90[CHB][hapmap]
rs1480364	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs1542574	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.98[LWK][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1552074	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs17051762	0.91[CEU][hapmap]
rs2061950	0.90[CHB][hapmap]
rs2127655	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2164599	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2170178	0.85[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2219890	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2219891	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2355943	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs2883809	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs3856932	0.86[CHB][hapmap]
rs4367100	0.90[CHB][hapmap];0.86[CHD][hapmap]
rs4687721	1.00[CEU][hapmap]
rs4687800	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974092	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974094	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974099	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs4974104	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4974105	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4974106	0.82[EUR][1000 genomes]
rs4974108	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs6445549	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445601	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445604	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6445611	0.90[CHB][hapmap];0.88[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs6445620	1.00[CEU][hapmap]
rs6445622	1.00[CEU][hapmap]
rs6445628	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6445727	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6772668	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6774745	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6784455	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs6796847	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs751075	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7614317	0.89[CHB][hapmap]
rs7616967	0.94[CHB][hapmap]
rs7617533	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7623803	0.87[ASN][1000 genomes]
rs7625006	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs7625821	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7630714	0.80[ASN][1000 genomes]
rs7633708	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7634799	0.90[CHB][hapmap]
rs7640083	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs7648012	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7649069	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs7651141	0.94[CHB][hapmap]
rs899750	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9832672	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9844581	0.90[CHB][hapmap]
rs9856566	0.94[CHB][hapmap]
rs9860403	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]
rs9877188	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs995543	0.90[CHB][hapmap];0.86[CHD][hapmap];0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2241784	TEX264	cis	Nerve Tibial	GTEx
rs2241784	IQCF2	cis	parietal	SCAN
rs2241784	HYAL2	cis	parietal	SCAN
rs2241784	HEMK1	cis	cerebellum	SCAN
rs2241784	TEX264	cis	Artery Tibial	GTEx
rs2241784	TEX264	cis	Esophagus Muscularis	GTEx
rs2241784	MST1	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51378600-51421000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:51378800-51421400	Weak transcription	Right Ventricle	heart
3	chr3:51384200-51420600	Weak transcription	Fetal Brain Male	brain
4	chr3:51392800-51418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:51406000-51420200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr3:51406000-51420400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:51406000-51420400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:51406000-51420600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:51406000-51420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:51406000-51420800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:51406000-51421400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:51406400-51420600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:51406400-51421600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:51410000-51421400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:51410400-51420600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:51410600-51419200	Weak transcription	Fetal Stomach	stomach
17	chr3:51411000-51420000	Strong transcription	Brain Cingulate Gyrus	brain
18	chr3:51411000-51420000	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr3:51411200-51420000	Strong transcription	Fetal Brain Female	brain
20	chr3:51412400-51420600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:51413800-51419800	Strong transcription	Stomach Smooth Muscle	stomach
22	chr3:51414400-51420600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:51414600-51419600	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:51414800-51421400	Weak transcription	HSMMtube	muscle
25	chr3:51415000-51419000	Weak transcription	Brain Substantia Nigra	brain
26	chr3:51415200-51421200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:51415400-51418400	Enhancers	Fetal Thymus	thymus
28	chr3:51415400-51420800	Weak transcription	Brain Anterior Caudate	brain
29	chr3:51415600-51420600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:51416400-51418600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:51416600-51419600	Strong transcription	Brain Hippocampus Middle	brain
32	chr3:51416600-51420800	Weak transcription	NHEK	skin
33	chr3:51416800-51419600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:51417000-51419400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:51417000-51420400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:51417000-51420600	Weak transcription	GM12878-XiMat	blood
37	chr3:51417200-51420600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr3:51417200-51421000	Weak transcription	HSMM	muscle
39	chr3:51417200-51421400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:51417400-51420600	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:51417400-51420800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:51417400-51420800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:51417600-51420600	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:51417600-51420800	Weak transcription	Primary T cells from cord blood	blood
45	chr3:51417600-51421400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:51417600-51421600	Weak transcription	Spleen	Spleen
47	chr3:51417800-51418600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr3:51417800-51418600	Enhancers	HepG2	liver
49	chr3:51417800-51420400	Weak transcription	Brain Germinal Matrix	brain
50	chr3:51417800-51421000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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