Variant report

Variant	rs10876041
Chromosome Location	chr12:50901882-50901883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50901773..50903761-chr12:50910341..50913326,3	MCF-7	breast:
2	chr12:50900950..50904807-chr12:50918762..50923043,5	MCF-7	breast:
3	chr12:50900701..50902991-chr12:51029876..51032348,2	MCF-7	breast:
4	chr12:50897453..50902823-chr12:51156009..51160960,8	MCF-7	breast:
5	chr12:50899485..50901952-chr12:50925003..50926748,2	MCF-7	breast:
6	chr12:50899807..50901324-chr12:50901368..50903053,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10735826	0.99[ASN][1000 genomes]
rs10747586	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10783366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10783367	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783368	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10783377	0.82[EUR][1000 genomes]
rs10876044	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876046	0.89[EUR][1000 genomes]
rs10876048	0.94[ASN][1000 genomes]
rs10876054	0.97[ASN][1000 genomes]
rs10876057	0.94[ASN][1000 genomes]
rs11609231	0.86[EUR][1000 genomes]
rs11611288	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs11614911	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832315	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12099615	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs12320201	0.90[ASN][1000 genomes]
rs12817256	0.94[ASN][1000 genomes]
rs12821270	0.90[EUR][1000 genomes]
rs13328926	0.98[ASN][1000 genomes]
rs1402693	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1521516	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs1521517	0.86[JPT][hapmap]
rs1996750	0.81[ASN][1000 genomes]
rs2251603	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs2252589	0.92[CEU][hapmap]
rs2252595	0.86[JPT][hapmap]
rs2684889	0.92[CEU][hapmap]
rs2684900	0.92[CEU][hapmap]
rs2684901	0.91[CEU][hapmap]
rs2684902	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs2684906	0.86[JPT][hapmap]
rs2700479	0.92[CEU][hapmap]
rs2700480	0.92[CEU][hapmap]
rs2700482	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2731439	0.92[CEU][hapmap]
rs2731440	0.95[CEU][hapmap]
rs2731442	0.91[CEU][hapmap]
rs2731443	0.92[CEU][hapmap];0.80[TSI][hapmap]
rs28414775	0.94[ASN][1000 genomes]
rs28479152	0.98[ASN][1000 genomes]
rs2947617	0.90[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4129355	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4306347	0.96[ASN][1000 genomes]
rs4517607	0.87[ASN][1000 genomes]
rs4562889	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4768848	0.90[ASN][1000 genomes]
rs4768885	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768887	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4768894	0.88[ASN][1000 genomes]
rs55939211	0.87[EUR][1000 genomes]
rs56089074	0.86[EUR][1000 genomes]
rs56104942	0.87[EUR][1000 genomes]
rs56753963	0.90[ASN][1000 genomes]
rs57512759	0.97[ASN][1000 genomes]
rs59194948	0.90[ASN][1000 genomes]
rs59683461	0.93[ASN][1000 genomes]
rs60239257	0.89[ASN][1000 genomes]
rs60494920	0.99[ASN][1000 genomes]
rs66597435	0.86[EUR][1000 genomes]
rs66644594	0.87[EUR][1000 genomes]
rs67701624	0.87[EUR][1000 genomes]
rs68171620	0.86[EUR][1000 genomes]
rs7131795	0.85[EUR][1000 genomes]
rs7131993	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7135222	0.90[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7300979	0.85[EUR][1000 genomes]
rs7301125	0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7302749	0.99[ASN][1000 genomes]
rs7305655	0.96[CEU][hapmap]
rs7306387	0.82[ASN][1000 genomes]
rs7307815	0.87[EUR][1000 genomes]
rs7487645	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7953880	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7955310	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs7957060	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978443	0.97[ASN][1000 genomes]
rs7979184	0.96[ASN][1000 genomes]
rs951591	0.86[JPT][hapmap]
rs9634264	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs9738596	0.89[ASN][1000 genomes]
rs9804759	0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10876041	LASS5	cis	cerebellum	SCAN
rs10876041	KIAA1463	cis	multi-tissue	Pritchard
rs10876041	DIP2B	cis	multi-tissue	Pritchard
rs10876041	KRT73	cis	parietal	SCAN
rs10876041	DIP2B	cis	cerebellum	SCAN
rs10876041	LASS5	cis	parietal	SCAN
rs10876041	DHH	cis	parietal	SCAN
rs10876041	CERS5	cis	Nerve Tibial	GTEx
rs10876041	LASS5	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50898200-50902200	Active TSS	Brain Angular Gyrus	brain
2	chr12:50899600-50903400	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr12:50899600-50903400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr12:50899800-50902600	Weak transcription	Lung	lung
5	chr12:50899800-50903600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
6	chr12:50900000-50902600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:50900000-50903000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:50900000-50903400	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr12:50900000-50903600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:50900000-50911000	Weak transcription	Colonic Mucosa	Colon
11	chr12:50900000-50911800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:50900000-50925400	Weak transcription	Esophagus	oesophagus
13	chr12:50900200-50902400	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr12:50900200-50902600	Enhancers	Fetal Brain Male	brain
15	chr12:50900200-50902800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr12:50900200-50903400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:50900200-50903800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr12:50900200-50903800	Enhancers	Stomach Mucosa	stomach
19	chr12:50900200-50904400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:50900200-50904400	Weak transcription	Aorta	Aorta
21	chr12:50900200-50906800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:50900200-50911200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:50900400-50902000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:50900400-50902200	Flanking Active TSS	HepG2	liver
25	chr12:50900400-50903000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:50900400-50904000	Enhancers	K562	blood
27	chr12:50900400-50910000	Weak transcription	Fetal Stomach	stomach
28	chr12:50900600-50902200	Enhancers	Thymus	Thymus
29	chr12:50900600-50902400	Flanking Active TSS	NHEK	skin
30	chr12:50900600-50902600	Enhancers	Colon Smooth Muscle	Colon
31	chr12:50900600-50903600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr12:50900600-50903800	Enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:50900600-50904600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:50900600-50916400	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:50900600-50932000	Weak transcription	Fetal Kidney	kidney
36	chr12:50900800-50902000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr12:50900800-50902000	Enhancers	Hela-S3	cervix
38	chr12:50900800-50902200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr12:50900800-50902400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:50900800-50902600	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:50900800-50902800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr12:50900800-50902800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:50900800-50903000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:50900800-50903200	Weak transcription	HSMMtube	muscle
45	chr12:50900800-50903600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr12:50900800-50908600	Weak transcription	Right Ventricle	heart
47	chr12:50900800-50911200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr12:50901000-50902800	Enhancers	A549	lung
49	chr12:50901000-50903400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:50901000-50903400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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