Variant report

Variant	rs10510761
Chromosome Location	chr3:52965255-52965256
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	BRCA1	chr3:52965247-52965258	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52946225..52948200-chr3:52964998..52966587,2	MCF-7	breast:
2	chr3:52963966..52966247-chr3:52967182..52969951,2	K562	blood:

Variant related genes	Relation type
SFMBT1	TF binding region

Extended variants
information (count: 127 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs11130329	0.87[GIH][hapmap]
rs11626	0.87[GIH][hapmap]
rs11705797	0.89[ASN][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707575	0.84[EUR][1000 genomes]
rs11707780	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11708337	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11710292	0.84[EUR][1000 genomes]
rs11710394	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11710707	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711773	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11712653	1.00[CEU][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713171	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713206	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713290	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11713324	0.87[GIH][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs11713376	0.89[ASN][1000 genomes]
rs11713479	0.82[AFR][1000 genomes]
rs11713859	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11714037	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714876	1.00[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs11714902	0.84[EUR][1000 genomes]
rs11715231	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715498	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11716506	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11716612	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11717132	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717619	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717715	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718388	0.89[EUR][1000 genomes]
rs11718538	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718752	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11718834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720191	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11720488	0.89[ASN][1000 genomes]
rs13058817	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13062228	0.89[ASN][1000 genomes]
rs13067373	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13068194	0.86[ASN][1000 genomes]
rs13069006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072457	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs13072818	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13074524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13076033	0.91[CEU][hapmap]
rs13078834	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13078971	0.84[EUR][1000 genomes]
rs13084937	0.84[EUR][1000 genomes]
rs13085514	0.84[EUR][1000 genomes]
rs13085544	0.81[EUR][1000 genomes]
rs13088281	0.92[MEX][hapmap]
rs13089969	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13091844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13092352	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095705	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13320044	0.84[EUR][1000 genomes]
rs1346719	1.00[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17052727	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2001732	0.87[GIH][hapmap]
rs2336540	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336541	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2564926	0.82[EUR][1000 genomes]
rs2581807	0.82[EUR][1000 genomes]
rs3097417	0.82[EUR][1000 genomes]
rs34121720	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34238610	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34244302	0.84[EUR][1000 genomes]
rs34313969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34340609	0.89[EUR][1000 genomes]
rs34493168	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34872575	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34933390	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34943350	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34979715	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35076015	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35163227	0.84[EUR][1000 genomes]
rs35174175	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35230793	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35378159	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35385050	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35404467	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35507120	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35569457	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs35720014	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35737577	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35849389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36090694	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36126605	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3733034	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[ASN][1000 genomes]
rs3733035	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3796352	1.00[CEU][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3806692	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3821872	0.89[EUR][1000 genomes]
rs4478072	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4608686	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs56231111	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs58515094	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58660500	0.89[EUR][1000 genomes]
rs59583591	0.84[EUR][1000 genomes]
rs60887045	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60942590	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61172708	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61473083	0.89[ASN][1000 genomes]
rs6445555	0.81[EUR][1000 genomes]
rs6445556	0.87[EUR][1000 genomes]
rs6445557	0.87[EUR][1000 genomes]
rs6762260	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6798472	0.87[GIH][hapmap]
rs71299622	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71299700	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71301804	0.87[EUR][1000 genomes]
rs71301808	0.89[EUR][1000 genomes]
rs71301809	0.84[EUR][1000 genomes]
rs71301811	0.82[EUR][1000 genomes]
rs71301814	0.84[EUR][1000 genomes]
rs71617204	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73839535	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs750474	1.00[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs7622420	0.84[EUR][1000 genomes]
rs7625448	0.84[EUR][1000 genomes]
rs7640293	0.84[EUR][1000 genomes]
rs7645611	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9756317	1.00[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs9875573	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10510761	ITIH4	cis	multi-tissue	Pritchard
rs10510761	TMEM110	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
2	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:52932200-52967800	Weak transcription	HSMM	muscle
6	chr3:52932200-52968600	Weak transcription	Osteobl	bone
7	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
9	chr3:52932400-52968600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr3:52932400-52968600	Weak transcription	NHDF-Ad	bronchial
11	chr3:52932400-52968800	Weak transcription	NHEK	skin
12	chr3:52935600-52968600	Strong transcription	Dnd41	blood
13	chr3:52941800-52980200	Weak transcription	Psoas Muscle	Psoas
14	chr3:52947400-52968000	Weak transcription	Fetal Lung	lung
15	chr3:52949000-52968800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:52950000-52966600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:52951200-52966400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52952000-52968600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:52952800-52965600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
21	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
22	chr3:52954400-52968600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:52954600-52967000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:52954800-52968400	Weak transcription	Brain Substantia Nigra	brain
25	chr3:52954800-52976800	Weak transcription	Brain Germinal Matrix	brain
26	chr3:52955200-52968600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:52955200-52968600	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:52955200-52986400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:52955800-52968800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:52956000-52968600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:52956000-52973800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr3:52956200-52968400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:52956400-52967600	Weak transcription	Fetal Brain Female	brain
34	chr3:52956400-52986400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr3:52957000-52967600	Weak transcription	Aorta	Aorta
36	chr3:52957200-52966600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr3:52957200-52974800	Weak transcription	Primary T cells from cord blood	blood
38	chr3:52958200-52985800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:52960200-52979600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr3:52960800-52966200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:52961200-52966400	Strong transcription	Placenta	Placenta
42	chr3:52961400-52968800	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:52961600-52987000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr3:52962200-52966200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:52962400-52967200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:52962400-52967400	Weak transcription	Right Ventricle	heart
47	chr3:52962400-52968400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:52962400-52968600	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:52962400-52968600	Weak transcription	A549	lung
50	chr3:52962400-52969800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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