Variant report

Variant	rs11169507
Chromosome Location	chr12:51015509-51015510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:51012150..51015682-chr12:51031873..51033630,3	MCF-7	breast:
2	chr12:51014624..51017594-chr12:51125519..51128159,2	MCF-7	breast:
3	chr12:51013472..51015886-chr12:51019988..51021681,3	K562	blood:
4	chr12:51010106..51013321-chr12:51014428..51017771,4	K562	blood:
5	chr12:50896850..50900155-chr12:51012799..51015925,4	K562	blood:
6	chr12:51014540..51016372-chr12:51084957..51086648,2	K562	blood:
7	chr12:51014321..51016158-chr12:51034710..51036636,2	MCF-7	breast:
8	chr12:51011830..51013610-chr12:51014850..51017833,2	MCF-7	breast:
9	chr12:50974887..50977469-chr12:51012857..51015766,3	MCF-7	breast:
10	chr12:50925165..50930036-chr12:51011670..51016786,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs1003033	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10431486	0.92[EUR][1000 genomes]
rs10431535	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10444547	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10459233	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10459234	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10459235	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10506294	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10506295	1.00[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10747584	0.89[EUR][1000 genomes]
rs10747585	0.92[EUR][1000 genomes]
rs10747587	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783369	0.91[EUR][1000 genomes]
rs10783370	0.92[EUR][1000 genomes]
rs10783371	0.92[EUR][1000 genomes]
rs10783372	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs10783373	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs10783374	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10783378	0.92[EUR][1000 genomes]
rs10783381	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783382	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783383	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10783384	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10783389	0.82[CHB][hapmap]
rs10876042	0.88[EUR][1000 genomes]
rs10876043	0.89[EUR][1000 genomes]
rs10876047	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[EUR][1000 genomes]
rs10876051	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs10876052	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs10876053	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs10876056	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[EUR][1000 genomes]
rs10876058	0.92[EUR][1000 genomes]
rs10876060	0.90[EUR][1000 genomes]
rs10876061	0.95[CHB][hapmap];0.92[EUR][1000 genomes]
rs10876063	0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10876065	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10876067	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10876068	0.86[AMR][1000 genomes]
rs10876070	1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876071	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876072	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10876073	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10876075	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876076	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10876096	0.82[CHB][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap]
rs10876097	0.82[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap]
rs11169479	1.00[CEU][hapmap];0.85[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169480	0.92[EUR][1000 genomes]
rs11169481	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[EUR][1000 genomes]
rs11169483	0.87[EUR][1000 genomes]
rs11169487	0.92[EUR][1000 genomes]
rs11169493	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs11169498	0.89[EUR][1000 genomes]
rs11169505	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11169515	1.00[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11169528	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169532	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169537	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11169538	0.93[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169539	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169544	1.00[GIH][hapmap]
rs11169552	0.82[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap]
rs11169560	0.82[CHB][hapmap]
rs11169561	0.81[CHB][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap]
rs11612002	0.84[CEU][hapmap]
rs11613488	1.00[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11615933	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12230242	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12231309	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12231317	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12580051	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12580479	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12582712	0.92[EUR][1000 genomes]
rs12809086	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12827022	0.89[EUR][1000 genomes]
rs1344958	0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs17124930	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2243571	0.84[EUR][1000 genomes]
rs2684908	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs2700478	0.86[EUR][1000 genomes]
rs34867510	0.88[EUR][1000 genomes]
rs35845404	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3742063	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3742064	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3809319	0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs3825402	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3893353	0.92[EUR][1000 genomes]
rs3935138	0.94[CEU][hapmap]
rs3935869	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4131769	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4238106	1.00[CEU][hapmap];0.90[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4238107	1.00[ASN][1000 genomes]
rs4238108	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4388959	0.81[CEU][hapmap]
rs4516034	0.92[EUR][1000 genomes]
rs4768850	0.92[EUR][1000 genomes]
rs4768852	0.91[EUR][1000 genomes]
rs4768853	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768858	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768866	0.81[CHB][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap]
rs4768884	0.92[EUR][1000 genomes]
rs4768888	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs4768889	0.92[EUR][1000 genomes]
rs4768890	0.81[EUR][1000 genomes]
rs4768892	0.92[EUR][1000 genomes]
rs4768893	0.95[CHB][hapmap];0.92[EUR][1000 genomes]
rs4768895	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4768899	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4768904	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4768906	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4768907	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768911	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4768912	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768913	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4768914	0.94[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4768922	0.82[CHB][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap]
rs4768975	1.00[CEU][hapmap]
rs55680342	0.90[EUR][1000 genomes]
rs55877451	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61926275	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6580761	0.90[CEU][hapmap]
rs7134976	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7138604	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[EUR][1000 genomes]
rs7305375	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7307419	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7316864	0.90[CEU][hapmap]
rs7956591	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes]
rs876078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876079	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876080	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs952318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9788159	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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	esv1822840	chr12:50973897-51015509	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11169507	KRT4	cis	cerebellum	SCAN
rs11169507	DIP2B	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50994600-51018600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:51006600-51016000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:51007000-51017600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr12:51008600-51015600	Weak transcription	HUVEC	blood vessel
5	chr12:51009800-51016000	Enhancers	HMEC	breast
6	chr12:51010400-51016400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr12:51012000-51016000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr12:51012000-51016200	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr12:51012000-51016600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:51012000-51016600	Enhancers	Fetal Intestine Large	intestine
11	chr12:51012000-51017800	Enhancers	Duodenum Mucosa	Duodenum
12	chr12:51012000-51020000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:51012000-51020200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:51012200-51016000	Enhancers	HepG2	liver
15	chr12:51012200-51016400	Enhancers	Fetal Heart	heart
16	chr12:51012200-51016400	Enhancers	Fetal Intestine Small	intestine
17	chr12:51012200-51019800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:51012400-51015600	Enhancers	Placenta	Placenta
19	chr12:51012400-51016400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr12:51012400-51016400	Enhancers	Primary T cells from cord blood	blood
21	chr12:51012600-51015600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr12:51012600-51016000	Enhancers	Right Atrium	heart
23	chr12:51012600-51016000	Enhancers	Small Intestine	intestine
24	chr12:51012600-51016000	Enhancers	Osteobl	bone
25	chr12:51012800-51015600	Enhancers	Brain Anterior Caudate	brain
26	chr12:51012800-51016000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:51012800-51016000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:51012800-51016000	Enhancers	Fetal Muscle Leg	muscle
29	chr12:51012800-51016000	Enhancers	Rectal Smooth Muscle	rectum
30	chr12:51012800-51016000	Enhancers	HSMMtube	muscle
31	chr12:51012800-51016000	Flanking Active TSS	NHEK	skin
32	chr12:51012800-51016200	Enhancers	Brain Germinal Matrix	brain
33	chr12:51012800-51018200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:51012800-51018400	Enhancers	Pancreas	Pancrea
35	chr12:51012800-51020200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:51013000-51016000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:51013000-51016000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:51013000-51016200	Enhancers	iPS-15b Cell Line	embryonic stem cell
39	chr12:51013000-51016200	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:51013000-51016400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:51013000-51019600	Enhancers	Fetal Thymus	thymus
42	chr12:51013000-51020000	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr12:51013200-51015600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr12:51013200-51015600	Enhancers	Right Ventricle	heart
45	chr12:51013200-51015800	Enhancers	NHLF	lung
46	chr12:51013200-51016000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:51013200-51016000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr12:51013200-51016000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr12:51013200-51016000	Enhancers	Left Ventricle	heart
50	chr12:51013400-51016000	Enhancers	Thymus	Thymus

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