Variant report

Variant	rs10876044
Chromosome Location	chr12:50906405-50906406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50897433..50902148-chr12:50902725..50909458,9	K562	blood:
2	chr12:50899429..50901096-chr12:50905405..50907049,2	MCF-7	breast:
3	chr12:50898616..50901375-chr12:50905321..50908963,4	K562	blood:
4	chr12:50897723..50903128-chr12:50904714..50906914,6	MCF-7	breast:
5	chr12:50905471..50907302-chr12:51036859..51038661,2	K562	blood:

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10735826	0.98[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];0.97[ASN][1000 genomes]
rs10783368	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10783377	0.82[EUR][1000 genomes]
rs10876041	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	0.93[ASN][1000 genomes]
rs10876054	0.96[ASN][1000 genomes]
rs10876057	0.93[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];0.99[ASN][1000 genomes]
rs11832315	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs12099615	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs12320201	0.90[ASN][1000 genomes]
rs12817256	0.93[ASN][1000 genomes]
rs12821270	0.90[EUR][1000 genomes]
rs13328926	0.97[ASN][1000 genomes]
rs1402693	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1521516	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs1521517	0.87[JPT][hapmap]
rs1996750	0.80[ASN][1000 genomes]
rs2251603	0.92[CEU][hapmap];0.83[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];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs2684906	0.87[JPT][hapmap]
rs2700479	0.92[CEU][hapmap]
rs2700480	0.92[CEU][hapmap]
rs2700482	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs2700485	0.92[CEU][hapmap]
rs2731439	0.92[CEU][hapmap]
rs2731440	0.96[CEU][hapmap]
rs2731442	0.92[CEU][hapmap]
rs2731443	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs28414775	0.93[ASN][1000 genomes]
rs28479152	0.97[ASN][1000 genomes]
rs2947617	0.90[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs4129355	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs4306347	0.96[ASN][1000 genomes]
rs4517607	0.87[ASN][1000 genomes]
rs4562889	0.90[CHB][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs4768886	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768887	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[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	0.96[ASN][1000 genomes]
rs59194948	0.90[ASN][1000 genomes]
rs59683461	0.92[ASN][1000 genomes]
rs60239257	0.88[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];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7135222	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7300979	0.85[EUR][1000 genomes]
rs7301125	0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.91[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];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs7953880	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7955310	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7957060	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7978443	0.96[ASN][1000 genomes]
rs7979184	0.96[ASN][1000 genomes]
rs951591	0.86[JPT][hapmap]
rs9634264	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9738596	0.88[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10876044	CERS5	cis	Nerve Tibial	GTEx
rs10876044	DIP2B	cis	cerebellum	SCAN
rs10876044	DIP2B	cis	multi-tissue	Pritchard
rs10876044	KIAA1463	cis	multi-tissue	Pritchard
rs10876044	LASS5	cis	multi-tissue	Pritchard
rs10876044	DIP2B	cis	Lymphoblastoid	GTEx
rs10876044	LASS5	cis	parietal	SCAN
rs10876044	DHH	cis	parietal	SCAN
rs10876044	LASS5	cis	cerebellum	SCAN
rs10876044	KRT73	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50900000-50911000	Weak transcription	Colonic Mucosa	Colon
2	chr12:50900000-50911800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:50900000-50925400	Weak transcription	Esophagus	oesophagus
4	chr12:50900200-50906800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:50900200-50911200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:50900400-50910000	Weak transcription	Fetal Stomach	stomach
7	chr12:50900600-50916400	Enhancers	Primary B cells from peripheral blood	blood
8	chr12:50900600-50932000	Weak transcription	Fetal Kidney	kidney
9	chr12:50900800-50908600	Weak transcription	Right Ventricle	heart
10	chr12:50900800-50911200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:50901000-50907000	Weak transcription	Ovary	ovary
12	chr12:50901000-50910800	Weak transcription	HUVEC	blood vessel
13	chr12:50901000-50911000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr12:50901400-50925600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:50901600-50915600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:50901800-50911000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr12:50902000-50909200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:50902200-50911200	Weak transcription	Dnd41	blood
19	chr12:50902400-50911000	Weak transcription	Fetal Lung	lung
20	chr12:50902600-50911200	Weak transcription	Fetal Brain Male	brain
21	chr12:50902800-50907400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:50902800-50908000	Weak transcription	Lung	lung
23	chr12:50902800-50912000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:50903200-50911200	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:50903400-50906800	Enhancers	Primary B cells from cord blood	blood
26	chr12:50903400-50908000	Weak transcription	Thymus	Thymus
27	chr12:50903400-50908200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:50903400-50908400	Weak transcription	Left Ventricle	heart
29	chr12:50903400-50910200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr12:50903400-50925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:50903600-50906600	Weak transcription	Spleen	Spleen
32	chr12:50903600-50907000	Weak transcription	Primary hematopoietic stem cells	blood
33	chr12:50903600-50907000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:50903600-50907400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:50903600-50908000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr12:50903600-50908200	Weak transcription	Fetal Thymus	thymus
37	chr12:50903600-50908200	Weak transcription	Small Intestine	intestine
38	chr12:50903600-50908400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr12:50903600-50908400	Weak transcription	Adipose Nuclei	Adipose
40	chr12:50903600-50908400	Weak transcription	Fetal Muscle Leg	muscle
41	chr12:50903600-50908600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:50903600-50908600	Weak transcription	Placenta	Placenta
43	chr12:50903600-50908600	Weak transcription	Right Atrium	heart
44	chr12:50903600-50909400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:50903600-50911200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:50903600-50911400	Weak transcription	Psoas Muscle	Psoas
47	chr12:50903600-50922800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:50903800-50906800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr12:50903800-50907200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:50903800-50908200	Weak transcription	Rectal Mucosa Donor 29	rectum

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