Variant report

Variant	rs6838718
Chromosome Location	chr4:53710828-53710829
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53705671..53708824-chr4:53710798..53715308,4	MCF-7	breast:
2	chr4:53707171..53710992-chr4:53726798..53730468,4	MCF-7	breast:
3	chr4:53709061..53711670-chr4:53726343..53729125,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10517269	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1109696	0.89[YRI][hapmap]
rs11932601	0.84[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs11938159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11939448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11941841	0.84[GIH][hapmap]
rs17082084	0.84[ASW][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap]
rs17082087	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17082091	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2007936	0.89[YRI][hapmap]
rs2007959	0.89[YRI][hapmap]
rs3811781	0.87[AMR][1000 genomes]
rs58461944	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58577680	0.80[AMR][1000 genomes]
rs59042894	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6554054	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6554056	0.84[GIH][hapmap]
rs6554057	0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes]
rs6817433	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6818178	0.92[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6848200	0.87[AMR][1000 genomes]
rs6858566	0.84[ASW][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.85[YRI][hapmap]
rs73814868	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73814886	0.85[AMR][1000 genomes]
rs7655781	0.82[JPT][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7663419	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670068	0.83[AMR][1000 genomes]
rs7685816	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7688141	0.81[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7693568	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7699960	0.85[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs881744	0.92[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.81[EUR][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	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6838718	CR2	trans	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53708400-53714000	Weak transcription	Fetal Intestine Small	intestine
2	chr4:53708400-53719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:53708600-53714000	Weak transcription	Esophagus	oesophagus
4	chr4:53708600-53714000	Weak transcription	Pancreas	Pancrea
5	chr4:53708600-53718000	Weak transcription	Lung	lung
6	chr4:53709000-53712800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:53709000-53718200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:53709200-53711200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr4:53709200-53712400	Weak transcription	Right Atrium	heart
10	chr4:53709200-53714000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:53709200-53714000	Weak transcription	Gastric	stomach
12	chr4:53709200-53714000	Weak transcription	Psoas Muscle	Psoas
13	chr4:53709200-53718000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:53709200-53718600	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:53709200-53718800	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:53709200-53718800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:53709400-53711000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:53709400-53712800	Weak transcription	Stomach Mucosa	stomach
19	chr4:53709400-53716000	Weak transcription	Fetal Heart	heart
20	chr4:53709400-53718400	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr4:53709400-53721000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:53709600-53714000	Weak transcription	Fetal Lung	lung
23	chr4:53709600-53714000	Weak transcription	Left Ventricle	heart
24	chr4:53709600-53718800	Weak transcription	Right Ventricle	heart
25	chr4:53710000-53711600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:53710000-53713800	Weak transcription	Fetal Kidney	kidney
27	chr4:53710000-53718600	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:53710400-53714000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:53710400-53718600	Weak transcription	Placenta	Placenta
30	chr4:53710600-53715200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:53710800-53718400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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