Variant report

Variant	rs33550
Chromosome Location	chr5:112319041-112319042
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	TEAD4	chr5:112318953-112319450	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:112238408..112240377-chr5:112318483..112320645,2	K562	blood:
2	chr5:112312385..112315007-chr5:112318753..112321264,2	MCF-7	breast:
3	chr5:112312383..112314551-chr5:112314826..112319334,4	MCF-7	breast:
4	chr5:112317791..112320092-chr5:112860829..112862554,2	K562	blood:

Variant related genes	Relation type
DCP2	TF binding region
ENSG00000172795	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10059599	0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs12516502	0.94[JPT][hapmap]
rs12719155	0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs2052484	0.83[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs2080896	0.94[JPT][hapmap]
rs2112452	0.83[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap]
rs2112453	0.87[CHD][hapmap];0.94[JPT][hapmap]
rs33543	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.92[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs33546	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33547	0.93[ASN][1000 genomes]
rs33553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs33556	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33562	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33563	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33565	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs33567	1.00[YRI][hapmap]
rs3733969	0.83[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs3857433	0.85[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap]
rs4260660	0.88[JPT][hapmap]
rs4705530	0.83[ASW][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705533	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4705743	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4705746	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs4705754	0.93[JPT][hapmap]
rs62366969	0.84[AFR][1000 genomes]
rs6594659	0.88[JPT][hapmap]
rs7447818	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7718810	0.94[JPT][hapmap]
rs878073	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs878076	0.90[CHD][hapmap];0.94[JPT][hapmap]
rs882253	0.88[CHD][hapmap];0.94[JPT][hapmap]
rs888844	0.91[JPT][hapmap]
rs9326869	0.92[CHB][hapmap];0.87[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs959949	0.93[JPT][hapmap]

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	nsv1029271	chr5:112113308-112325943	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1019756	chr5:112242315-112325943	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1028759	chr5:112300490-112358514	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs33550	XRCC1	trans	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112313200-112329000	Weak transcription	Spleen	Spleen
2	chr5:112313800-112337600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:112314000-112320000	Weak transcription	Pancreas	Pancrea
4	chr5:112314000-112329000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:112314000-112335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:112314000-112337200	Weak transcription	Lung	lung
7	chr5:112314000-112338200	Weak transcription	Gastric	stomach
8	chr5:112314200-112319800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr5:112314200-112326800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr5:112314200-112328800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:112314200-112328800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:112314200-112332000	Weak transcription	Fetal Kidney	kidney
13	chr5:112314200-112332000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr5:112314200-112337000	Weak transcription	HSMMtube	muscle
15	chr5:112314200-112338200	Weak transcription	Aorta	Aorta
16	chr5:112314200-112341000	Weak transcription	Small Intestine	intestine
17	chr5:112314200-112349600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr5:112314200-112356800	Weak transcription	Stomach Mucosa	stomach
19	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
20	chr5:112314400-112322400	Weak transcription	Thymus	Thymus
21	chr5:112314400-112338400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:112314800-112320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr5:112314800-112322400	Weak transcription	Liver	Liver
24	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:112314800-112324400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:112314800-112325800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:112314800-112332000	Weak transcription	Brain Hippocampus Middle	brain
28	chr5:112314800-112332000	Weak transcription	NHLF	lung
29	chr5:112314800-112332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr5:112314800-112337200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr5:112314800-112349200	Weak transcription	Brain Substantia Nigra	brain
32	chr5:112315400-112330800	Weak transcription	Brain Anterior Caudate	brain
33	chr5:112315600-112328600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:112315600-112332000	Weak transcription	NHDF-Ad	bronchial
35	chr5:112315600-112332200	Weak transcription	Ovary	ovary
36	chr5:112315600-112339400	Weak transcription	Hela-S3	cervix
37	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
38	chr5:112315800-112319200	Weak transcription	HUVEC	blood vessel
39	chr5:112315800-112319600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr5:112315800-112329200	Weak transcription	Colon Smooth Muscle	Colon
41	chr5:112315800-112334600	Weak transcription	Brain Germinal Matrix	brain
42	chr5:112316000-112332200	Weak transcription	Fetal Brain Female	brain
43	chr5:112316000-112337000	Weak transcription	A549	lung
44	chr5:112316200-112319800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr5:112316200-112324600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:112316400-112319400	Genic enhancers	Dnd41	blood
47	chr5:112316400-112324200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr5:112316400-112330000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr5:112316600-112320000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:112316600-112320400	Strong transcription	Fetal Thymus	thymus

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