Variant report

Variant	rs3935869
Chromosome Location	chr12:50964076-50964077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50961532..50964619-chr12:50967406..50969791,3	MCF-7	breast:
2	chr12:50963922..50966119-chr12:50973720..50976501,2	MCF-7	breast:
3	chr12:50959640..50961996-chr12:50963303..50966253,2	MCF-7	breast:
4	chr12:50963836..50966336-chr12:51007234..51009900,2	MCF-7	breast:

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10431486	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10431535	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10444547	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10459233	0.94[EUR][1000 genomes]
rs10459234	0.80[EUR][1000 genomes]
rs10459235	0.83[EUR][1000 genomes]
rs10506294	0.83[EUR][1000 genomes]
rs10506295	0.82[EUR][1000 genomes]
rs10747584	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10747585	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747587	0.83[EUR][1000 genomes]
rs10783369	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783370	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783371	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10783372	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783373	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783374	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783375	0.84[EUR][1000 genomes]
rs10783378	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783381	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783382	0.84[EUR][1000 genomes]
rs10783383	0.83[EUR][1000 genomes]
rs10783384	0.82[EUR][1000 genomes]
rs10876042	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10876043	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876047	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876051	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876052	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876053	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876056	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876058	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876060	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876061	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876063	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876064	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10876065	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876067	0.82[ASN][1000 genomes]
rs10876068	0.82[AFR][1000 genomes]
rs10876070	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876071	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10876072	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876073	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10876075	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10876076	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169457	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169479	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169480	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169481	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169483	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169487	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169493	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169498	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169505	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169507	0.80[AMR][1000 genomes];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	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11615933	0.83[EUR][1000 genomes]
rs12230242	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12231309	0.86[EUR][1000 genomes]
rs12231317	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12580051	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12582712	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12809086	0.83[EUR][1000 genomes]
rs12827022	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124930	0.82[EUR][1000 genomes]
rs34867510	0.93[EUR][1000 genomes]
rs3893353	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3935138	0.84[EUR][1000 genomes]
rs4131769	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238106	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4238108	0.83[EUR][1000 genomes]
rs4516034	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768850	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768852	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768853	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768858	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4768884	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768888	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768889	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768890	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768892	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768893	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4768895	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768899	0.81[AMR][1000 genomes];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	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55877451	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61926275	0.83[EUR][1000 genomes]
rs67092086	0.84[EUR][1000 genomes]
rs7134976	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7138604	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307419	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7316864	0.84[EUR][1000 genomes]
rs7397999	0.84[EUR][1000 genomes]
rs7956591	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876078	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs876079	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs952318	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9788159	0.80[AMR][1000 genomes];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:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50945200-50965200	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:50948400-50966000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:50949400-50973600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:50953400-50965600	Weak transcription	Primary B cells from cord blood	blood
5	chr12:50953800-50966000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:50957200-50965600	Weak transcription	Psoas Muscle	Psoas
7	chr12:50957600-50969200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:50958800-50966000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:50959000-50976800	Weak transcription	Primary T cells from cord blood	blood
10	chr12:50959400-50966200	Weak transcription	K562	blood
11	chr12:50959800-50969800	Enhancers	Liver	Liver
12	chr12:50961000-50964600	Enhancers	HepG2	liver
13	chr12:50961400-50964200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr12:50961400-50964400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:50961600-50964400	Enhancers	Stomach Mucosa	stomach
16	chr12:50961600-50969400	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr12:50961800-50964200	Enhancers	Brain Anterior Caudate	brain
18	chr12:50961800-50964200	Enhancers	NHEK	skin
19	chr12:50961800-50964400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:50961800-50964400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:50961800-50964400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:50961800-50964400	Enhancers	Colon Smooth Muscle	Colon
23	chr12:50961800-50964600	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr12:50961800-50967000	Weak transcription	Thymus	Thymus
25	chr12:50961800-50969600	Enhancers	Adipose Nuclei	Adipose
26	chr12:50961800-50971200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:50962000-50964200	Enhancers	Rectal Smooth Muscle	rectum
28	chr12:50962000-50964400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:50962000-50966600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:50962000-50968400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:50962200-50965800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:50962200-50966600	Weak transcription	Fetal Intestine Large	intestine
33	chr12:50962200-50966600	Weak transcription	Right Ventricle	heart
34	chr12:50962200-50968200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:50962200-50968200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:50962200-50968200	Weak transcription	Esophagus	oesophagus
37	chr12:50962200-50969200	Weak transcription	Lung	lung
38	chr12:50962400-50964600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:50962400-50964600	Enhancers	Brain Hippocampus Middle	brain
40	chr12:50962400-50965600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr12:50962400-50965600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:50962400-50965600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:50962400-50965600	Weak transcription	GM12878-XiMat	blood
44	chr12:50962400-50965800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:50962400-50966200	Weak transcription	Fetal Intestine Small	intestine
46	chr12:50962400-50966200	Weak transcription	Spleen	Spleen
47	chr12:50962400-50966600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:50962400-50966600	Weak transcription	Aorta	Aorta
49	chr12:50962400-50966600	Weak transcription	Fetal Brain Male	brain
50	chr12:50962400-50966600	Weak transcription	Gastric	stomach

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