Variant report

Variant	rs10057103
Chromosome Location	chr5:43609343-43609344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr5:43609310-43609369	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:43554479..43560281-chr5:43606436..43612710,12	MCF-7	breast:
2	chr5:43563571..43565938-chr5:43608423..43610128,2	K562	blood:
3	chr5:43606933..43611774-chr5:43612584..43615643,4	MCF-7	breast:
4	chr5:43604308..43606276-chr5:43607859..43609785,3	MCF-7	breast:
5	chr5:43556272..43559075-chr5:43608717..43610456,2	K562	blood:
6	chr5:43601278..43604489-chr5:43608532..43612501,5	MCF-7	breast:
7	chr5:43605782..43611658-chr5:43611810..43617296,10	K562	blood:

No data

Variant related genes	Relation type
NNT	TF binding region
ENSG00000172239	Chromatin interaction
ENSG00000112992	Chromatin interaction
ENSG00000248092	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10036954	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs10038608	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10042992	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs10055801	0.96[MEX][hapmap]
rs10058558	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10059993	0.96[MEX][hapmap]
rs10061165	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs10065689	0.96[MEX][hapmap]
rs10065863	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10074682	0.85[CEU][hapmap];1.00[MEX][hapmap]
rs10447144	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10462051	0.85[CEU][hapmap]
rs1072745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1072746	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941640	0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs11949083	0.96[MEX][hapmap]
rs12521249	0.96[MEX][hapmap]
rs12652547	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs13189004	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13360902	0.82[ASN][1000 genomes]
rs1366410	0.96[MEX][hapmap]
rs1389868	0.85[CEU][hapmap]
rs1428640	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2172763	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs35881272	0.82[AFR][1000 genomes]
rs3776423	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs3806870	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs4072918	0.96[MEX][hapmap]
rs4072919	0.91[MEX][hapmap]
rs4073848	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4074777	0.96[MEX][hapmap]
rs4242099	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4367306	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[AFR][1000 genomes]
rs4386738	0.96[MEX][hapmap]
rs4467713	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs4513704	0.87[AFR][1000 genomes]
rs4535459	0.91[MEX][hapmap]
rs4610465	0.85[ASN][1000 genomes]
rs4866752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4866833	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs4991951	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55641556	0.81[ASN][1000 genomes]
rs56400900	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6451692	0.89[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs6451695	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs6451696	0.85[CEU][hapmap];0.96[MEX][hapmap]
rs6451698	0.85[CEU][hapmap];0.83[MEX][hapmap]
rs6451706	0.87[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs6451718	0.87[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6860493	0.96[MEX][hapmap]
rs6862102	0.84[CEU][hapmap]
rs6870018	0.85[CEU][hapmap]
rs6878770	0.96[MEX][hapmap]
rs6883661	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6884661	0.96[MEX][hapmap]
rs6885679	0.96[MEX][hapmap]
rs6895327	0.96[MEX][hapmap]
rs6896693	0.96[MEX][hapmap]
rs750582	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs750584	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7701429	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7703662	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs7708072	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708369	0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7710125	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7710628	0.91[MEX][hapmap]
rs7713479	0.96[MEX][hapmap]
rs7715782	0.95[MEX][hapmap]
rs7718627	0.95[MEX][hapmap]
rs7724571	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7732656	0.96[MEX][hapmap]
rs7737793	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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	220 gene(s)	inside rSNPs	diseases
3	nsv881108	chr5:43527432-43800333	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10057103	YY2	trans	cerebellum	SCAN
rs10057103	C5orf34	cis	parietal	SCAN
rs10057103	MGC42105	cis	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43604200-43631200	Weak transcription	A549	lung
2	chr5:43604400-43609800	Weak transcription	Ovary	ovary
3	chr5:43604400-43613000	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr5:43604400-43613400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:43604400-43619400	Weak transcription	Placenta	Placenta
6	chr5:43604400-43619600	Weak transcription	HMEC	breast
7	chr5:43604400-43631200	Weak transcription	Pancreas	Pancrea
8	chr5:43604400-43635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:43604400-43649200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:43604400-43649200	Weak transcription	Esophagus	oesophagus
11	chr5:43604400-43660600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:43604600-43609400	Weak transcription	HSMMtube	muscle
13	chr5:43604600-43609400	Weak transcription	Osteobl	bone
14	chr5:43604600-43609600	Weak transcription	Fetal Kidney	kidney
15	chr5:43604600-43609600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr5:43604600-43609800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:43604600-43609800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:43604600-43609800	Weak transcription	Fetal Intestine Large	intestine
19	chr5:43604600-43611200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:43604600-43611400	Weak transcription	Hela-S3	cervix
21	chr5:43604600-43612000	Weak transcription	Aorta	Aorta
22	chr5:43604600-43614000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:43604600-43624400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:43604600-43649800	Weak transcription	Colonic Mucosa	Colon
25	chr5:43604800-43609400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr5:43604800-43609400	Weak transcription	NHLF	lung
27	chr5:43604800-43609600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:43604800-43609600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:43604800-43609600	Weak transcription	Brain Hippocampus Middle	brain
30	chr5:43604800-43609600	Weak transcription	Fetal Lung	lung
31	chr5:43604800-43609600	Weak transcription	HSMM	muscle
32	chr5:43604800-43609800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr5:43604800-43612200	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:43604800-43612200	Weak transcription	NH-A	brain
35	chr5:43604800-43612400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:43604800-43613400	Weak transcription	Brain Substantia Nigra	brain
37	chr5:43604800-43630200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr5:43604800-43630800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr5:43604800-43635400	Weak transcription	Gastric	stomach
40	chr5:43604800-43635400	Weak transcription	Spleen	Spleen
41	chr5:43604800-43649800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:43605000-43609600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:43605000-43609800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:43605000-43609800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr5:43605000-43609800	Weak transcription	Right Ventricle	heart
46	chr5:43605000-43609800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:43605000-43613400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:43605000-43631200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:43605000-43631400	Weak transcription	Lung	lung
50	chr5:43605000-43656000	Weak transcription	Small Intestine	intestine

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