Variant report

Variant	rs1949733
Chromosome Location	chr4:8503359-8503360
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8500815..8505571-chr4:8524859..8530536,4	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10461079	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1357481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543246	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1880023	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1880024	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1916326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2010758	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2140337	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255501	0.85[EUR][1000 genomes]
rs2386227	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2450475	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631731	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2631734	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2631735	0.86[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs2631736	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2631740	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2631742	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631743	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631744	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2631745	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631746	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631754	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2631756	0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2631758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631762	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688223	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688224	0.83[AMR][1000 genomes]
rs2688227	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688231	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688233	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688235	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688242	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2688243	1.00[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2688247	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3103067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3103069	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3103070	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103071	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103072	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3103099	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4696828	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6447875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6837429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6845969	0.90[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs6858542	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs868105	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871768	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs940133	1.00[CEU][hapmap];0.89[YRI][hapmap];0.97[EUR][1000 genomes]
rs940134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs940136	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3377450	chr4:8502852-8506150	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Response to antineoplastic agents	21659360	GWAS catalog

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1949733	TBC1D14	cis	parietal	SCAN
rs1949733	ACOX3	Cis_1M	lymphoblastoid	RTeQTL
rs1949733	GPR78	cis	parietal	SCAN
rs1949733	C4orf23	cis	parietal	SCAN
rs1949733	TRMT44	cis	Nerve Tibial	GTEx
rs1949733	EVC	cis	parietal	SCAN
rs1949733	ACOX3	cis	lymphoblastoid	seeQTL
rs1949733	C4orf23	cis	cerebellum	SCAN
rs1949733	RP11-689P11.2	cis	lung	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8491000-8505200	Weak transcription	Fetal Brain Female	brain
2	chr4:8497000-8504200	Weak transcription	Right Atrium	heart
3	chr4:8501600-8503600	Weak transcription	Adipose Nuclei	Adipose
4	chr4:8501600-8504000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:8501600-8504000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr4:8501600-8504000	Weak transcription	Fetal Heart	heart
7	chr4:8501600-8504200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:8501600-8504200	Weak transcription	Esophagus	oesophagus
9	chr4:8501600-8504200	Weak transcription	Pancreas	Pancrea
10	chr4:8501600-8504400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:8501600-8504400	Weak transcription	Lung	lung
12	chr4:8501600-8504600	Weak transcription	Brain Anterior Caudate	brain
13	chr4:8501600-8504600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:8501600-8505200	Weak transcription	Brain Substantia Nigra	brain
15	chr4:8501600-8505600	Weak transcription	Gastric	stomach
16	chr4:8501600-8505800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:8501600-8505800	Weak transcription	Colonic Mucosa	Colon
18	chr4:8501600-8505800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:8501600-8506000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr4:8501600-8507000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:8501600-8507000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:8501600-8507400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:8501600-8507400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr4:8501600-8507600	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:8501600-8507600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:8501600-8507600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:8501600-8507800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:8501600-8507800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr4:8501600-8507800	Weak transcription	Brain Angular Gyrus	brain
30	chr4:8501800-8510600	Enhancers	Ovary	ovary
31	chr4:8502600-8504000	Enhancers	Fetal Muscle Leg	muscle
32	chr4:8502800-8504800	Enhancers	HSMMtube	muscle
33	chr4:8502800-8505800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr4:8502800-8512800	Enhancers	Placenta	Placenta
35	chr4:8503000-8503400	Bivalent Enhancer	HepG2	liver
36	chr4:8503000-8504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:8503000-8504200	Enhancers	Fetal Muscle Trunk	muscle
38	chr4:8503000-8505400	Enhancers	HSMM	muscle
39	chr4:8503000-8506800	Enhancers	Brain Hippocampus Middle	brain

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