Variant report

Variant	rs3088168
Chromosome Location	chr11:35273268-35273269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:35260075..35262709-chr11:35271623..35274355,2	K562	blood:
2	chr11:35262350..35264574-chr11:35271788..35273676,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1043101	0.90[ASW][hapmap];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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742339	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10742340	0.92[EUR][1000 genomes]
rs10742341	0.92[EUR][1000 genomes]
rs10768118	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10768120	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10768121	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10768122	0.90[ASW][hapmap];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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10768123	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10768126	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10836356	1.00[ASN][1000 genomes]
rs10836360	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10836361	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10836362	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10836363	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10836364	0.90[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10836367	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10836369	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11033045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11524863	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12361171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12796856	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1570214	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1570215	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17378105	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35629461	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3763888	1.00[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794086	0.92[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs3794089	0.90[ASW][hapmap];0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs3794090	0.90[EUR][1000 genomes]
rs3794091	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3794098	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794099	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794100	1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794101	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794102	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3794103	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3847604	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4755394	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4755395	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4756203	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4756204	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4756205	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4756206	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57339940	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6484778	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7105505	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7105690	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7121587	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs736374	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7946149	0.92[EUR][1000 genomes]
rs932633	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs932635	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs957350	0.83[EUR][1000 genomes]
rs9633870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv541004	chr11:35122694-35297414	Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3088168	HIPK3	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35264400-35281800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:35264800-35281800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:35265800-35305800	Weak transcription	HepG2	liver
4	chr11:35267800-35276200	Weak transcription	Right Atrium	heart
5	chr11:35268600-35274400	Weak transcription	Osteobl	bone
6	chr11:35269000-35274200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr11:35269400-35281800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr11:35270200-35278200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr11:35270200-35292600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr11:35270400-35273800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr11:35270400-35273800	Weak transcription	NHLF	lung
12	chr11:35270400-35274000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:35270400-35274000	Weak transcription	NHDF-Ad	bronchial
14	chr11:35270400-35274600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:35270400-35274800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:35270400-35275000	Weak transcription	Colon Smooth Muscle	Colon
17	chr11:35270400-35277600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:35270400-35277600	Weak transcription	Brain Anterior Caudate	brain
19	chr11:35270400-35285400	Weak transcription	Brain Germinal Matrix	brain
20	chr11:35270400-35296400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:35270400-35307000	Weak transcription	Fetal Brain Male	brain
22	chr11:35270600-35275800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr11:35270600-35277600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr11:35270600-35277600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr11:35270600-35278000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr11:35270600-35278000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr11:35270600-35281000	Weak transcription	Fetal Brain Female	brain
28	chr11:35270600-35284400	Weak transcription	Brain Hippocampus Middle	brain
29	chr11:35271200-35277400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:35271200-35286400	Weak transcription	Pancreas	Pancrea
31	chr11:35271600-35275800	Weak transcription	Aorta	Aorta
32	chr11:35272400-35274200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr11:35272600-35278000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr11:35272800-35277000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:35273000-35273400	Weak transcription	Monocytes-CD14+_RO01746	blood

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