Variant report

Variant	rs11169498
Chromosome Location	chr12:50969179-50969180
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50925117..50926635-chr12:50967377..50969450,2	MCF-7	breast:
2	chr12:50961532..50964619-chr12:50967406..50969791,3	MCF-7	breast:
3	chr12:50898767..50900607-chr12:50969120..50971692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10431486	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10431535	0.85[EUR][1000 genomes]
rs10444547	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10459233	0.94[EUR][1000 genomes]
rs10459235	0.83[EUR][1000 genomes]
rs10506294	0.83[EUR][1000 genomes]
rs10506295	0.82[EUR][1000 genomes]
rs10747584	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10747585	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747587	0.83[EUR][1000 genomes]
rs10783369	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783370	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783371	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783372	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783373	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783374	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783375	0.85[EUR][1000 genomes]
rs10783378	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783381	0.89[EUR][1000 genomes]
rs10783382	0.84[EUR][1000 genomes]
rs10783383	0.83[EUR][1000 genomes]
rs10783384	0.82[EUR][1000 genomes]
rs10876042	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10876043	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10876047	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876051	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876052	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876053	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10876056	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10876058	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876060	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876061	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876063	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876064	0.81[EUR][1000 genomes]
rs10876065	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876067	0.82[ASN][1000 genomes]
rs10876070	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876071	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876072	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876073	0.88[EUR][1000 genomes]
rs10876075	0.87[EUR][1000 genomes]
rs10876076	0.87[EUR][1000 genomes]
rs11169457	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169479	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169480	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169481	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169483	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169487	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169493	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169505	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169507	0.89[EUR][1000 genomes]
rs11169515	0.84[EUR][1000 genomes]
rs11169528	0.83[EUR][1000 genomes]
rs11169532	0.82[EUR][1000 genomes]
rs11169537	0.82[EUR][1000 genomes]
rs11613488	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11615933	0.83[EUR][1000 genomes]
rs12230242	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12231309	0.86[EUR][1000 genomes]
rs12231317	0.87[EUR][1000 genomes]
rs12580051	0.87[EUR][1000 genomes]
rs12582712	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12809086	0.83[EUR][1000 genomes]
rs12827022	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17124930	0.82[EUR][1000 genomes]
rs34867510	0.93[EUR][1000 genomes]
rs3893353	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3935138	0.85[EUR][1000 genomes]
rs3935869	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4131769	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4238106	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4238108	0.83[EUR][1000 genomes]
rs4516034	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768850	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768852	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768853	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768858	0.87[EUR][1000 genomes]
rs4768884	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768888	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4768889	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768890	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768892	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768893	0.97[EUR][1000 genomes]
rs4768895	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4768899	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4768906	0.82[EUR][1000 genomes]
rs4768907	0.82[EUR][1000 genomes]
rs4768912	0.81[EUR][1000 genomes]
rs4768913	0.81[EUR][1000 genomes]
rs55680342	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55877451	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61926275	0.83[EUR][1000 genomes]
rs67092086	0.85[EUR][1000 genomes]
rs7134976	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7138604	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307419	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316864	0.85[EUR][1000 genomes]
rs7397999	0.85[EUR][1000 genomes]
rs7956591	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs876078	0.87[EUR][1000 genomes]
rs876079	0.87[EUR][1000 genomes]
rs952318	0.88[EUR][1000 genomes]
rs9788159	0.87[EUR][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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50949400-50973600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:50957600-50969200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:50959000-50976800	Weak transcription	Primary T cells from cord blood	blood
4	chr12:50959800-50969800	Enhancers	Liver	Liver
5	chr12:50961600-50969400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:50961800-50969600	Enhancers	Adipose Nuclei	Adipose
7	chr12:50961800-50971200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:50962200-50969200	Weak transcription	Lung	lung
9	chr12:50962400-50973600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:50962400-50983200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:50963400-50969200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:50964200-50970400	Enhancers	Placenta	Placenta
13	chr12:50965600-50969200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:50965600-50969400	Enhancers	HMEC	breast
15	chr12:50965600-50969600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:50965600-50969600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:50965600-50969600	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:50965600-50969600	Enhancers	Brain Hippocampus Middle	brain
19	chr12:50965600-50969600	Enhancers	GM12878-XiMat	blood
20	chr12:50965600-50969600	Enhancers	NHEK	skin
21	chr12:50965600-50969800	Enhancers	Colon Smooth Muscle	Colon
22	chr12:50965600-50969800	Enhancers	Fetal Muscle Leg	muscle
23	chr12:50965600-50970000	Enhancers	HepG2	liver
24	chr12:50965800-50969600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:50965800-50969600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:50965800-50969800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:50966000-50969600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr12:50966000-50969800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:50966000-50969800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:50966200-50969400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr12:50966200-50969600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr12:50966200-50970800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr12:50966200-50973400	Weak transcription	Primary B cells from cord blood	blood
34	chr12:50966400-50969200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr12:50966400-50969800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:50966600-50969200	Enhancers	Brain Germinal Matrix	brain
37	chr12:50966600-50969600	Enhancers	H1 Cell Line	embryonic stem cell
38	chr12:50966600-50969600	Enhancers	Fetal Intestine Large	intestine
39	chr12:50966600-50969800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:50966600-50969800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:50966800-50975600	Weak transcription	HSMM	muscle
42	chr12:50967000-50969200	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr12:50967000-50969400	Enhancers	Hela-S3	cervix
44	chr12:50967200-50978400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:50967200-50983000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr12:50967400-50972000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:50967400-50973600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:50967400-50991200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr12:50967400-50991200	Weak transcription	Aorta	Aorta
50	chr12:50967600-50972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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