Variant report

Variant	rs1683199
Chromosome Location	chr12:42490475-42490476
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	chr12:42474170..42476425-chr12:42489656..42492488,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009721	1.00[EUR][1000 genomes]
rs11118	0.87[MKK][hapmap];0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs1157577	1.00[EUR][1000 genomes]
rs11829542	1.00[EUR][1000 genomes]
rs11830248	1.00[EUR][1000 genomes]
rs11836064	1.00[EUR][1000 genomes]
rs1233989	1.00[EUR][1000 genomes]
rs1233991	1.00[EUR][1000 genomes]
rs1233993	1.00[EUR][1000 genomes]
rs1234007	1.00[EUR][1000 genomes]
rs1234031	1.00[EUR][1000 genomes]
rs1234041	1.00[EUR][1000 genomes]
rs1234103	1.00[EUR][1000 genomes]
rs1238283	1.00[EUR][1000 genomes]
rs1626596	1.00[EUR][1000 genomes]
rs1628339	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1683203	1.00[EUR][1000 genomes]
rs1688846	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1688876	1.00[EUR][1000 genomes]
rs17091023	1.00[EUR][1000 genomes]
rs1873684	1.00[EUR][1000 genomes]
rs1920698	1.00[EUR][1000 genomes]
rs2639131	1.00[EUR][1000 genomes]
rs56220552	1.00[EUR][1000 genomes]
rs57435495	1.00[EUR][1000 genomes]
rs58689889	1.00[EUR][1000 genomes]
rs59909142	1.00[EUR][1000 genomes]
rs7305651	1.00[EUR][1000 genomes]
rs73276375	1.00[EUR][1000 genomes]
rs73276381	1.00[EUR][1000 genomes]
rs73276390	1.00[EUR][1000 genomes]
rs73276399	1.00[EUR][1000 genomes]
rs73278206	1.00[EUR][1000 genomes]
rs73278217	1.00[EUR][1000 genomes]
rs73278222	1.00[EUR][1000 genomes]
rs73278223	1.00[EUR][1000 genomes]
rs73278224	1.00[EUR][1000 genomes]
rs73278227	1.00[EUR][1000 genomes]
rs73278230	1.00[EUR][1000 genomes]
rs73278244	1.00[EUR][1000 genomes]
rs73278291	1.00[EUR][1000 genomes]
rs73280009	1.00[EUR][1000 genomes]
rs73280011	1.00[EUR][1000 genomes]
rs73281814	1.00[EUR][1000 genomes]
rs73281820	1.00[EUR][1000 genomes]
rs73281838	1.00[EUR][1000 genomes]
rs73281851	1.00[EUR][1000 genomes]
rs73281860	1.00[EUR][1000 genomes]
rs73281880	1.00[EUR][1000 genomes]
rs73281886	1.00[EUR][1000 genomes]
rs73281894	1.00[EUR][1000 genomes]
rs73283707	1.00[EUR][1000 genomes]
rs73283734	1.00[EUR][1000 genomes]
rs73283759	1.00[EUR][1000 genomes]
rs73283792	1.00[EUR][1000 genomes]
rs74077430	1.00[EUR][1000 genomes]
rs7970895	1.00[EUR][1000 genomes]
rs824690	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824696	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824698	1.00[EUR][1000 genomes]
rs824715	1.00[EUR][1000 genomes]
rs824719	0.93[MKK][hapmap];0.88[YRI][hapmap];1.00[EUR][1000 genomes]
rs824720	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs824721	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824723	1.00[EUR][1000 genomes]
rs824725	1.00[EUR][1000 genomes]
rs824727	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824728	0.82[AFR][1000 genomes]
rs824729	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824731	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824732	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824733	1.00[EUR][1000 genomes]
rs824735	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs824737	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs844045	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs850964	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs850965	0.87[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1047830	chr12:42466192-42497603	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv2025559	chr12:42481619-42491335	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42469400-42491800	Weak transcription	Ovary	ovary
2	chr12:42470600-42491400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:42471000-42504200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:42471800-42524400	Weak transcription	Esophagus	oesophagus
5	chr12:42474000-42496000	Weak transcription	Fetal Intestine Large	intestine
6	chr12:42474200-42490600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr12:42474600-42514400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:42474600-42518800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:42474800-42491800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:42475000-42491800	Weak transcription	Brain Substantia Nigra	brain
11	chr12:42476000-42524400	Weak transcription	Gastric	stomach
12	chr12:42476200-42524400	Weak transcription	Pancreas	Pancrea
13	chr12:42476600-42523800	Weak transcription	Hela-S3	cervix
14	chr12:42478000-42505000	Weak transcription	Lung	lung
15	chr12:42478600-42511600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:42479200-42496800	Weak transcription	Psoas Muscle	Psoas
17	chr12:42479600-42505400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:42480000-42492400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:42480200-42492000	Weak transcription	Brain Hippocampus Middle	brain
20	chr12:42480200-42505600	Weak transcription	Fetal Lung	lung
21	chr12:42480200-42512000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:42480600-42491600	Weak transcription	Fetal Heart	heart
23	chr12:42480600-42504600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:42481600-42491200	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:42481800-42491400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:42483000-42502800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr12:42483200-42499200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:42483600-42511400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:42484200-42504000	Weak transcription	Placenta	Placenta
30	chr12:42484400-42524800	Weak transcription	Right Ventricle	heart
31	chr12:42484600-42491000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr12:42484600-42498800	Weak transcription	Fetal Kidney	kidney
33	chr12:42484800-42496200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:42484800-42497400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:42485000-42491800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:42485000-42491800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:42485000-42504000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:42485200-42511600	Weak transcription	NHDF-Ad	bronchial
39	chr12:42485600-42498400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr12:42485800-42491800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:42485800-42501400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:42485800-42512200	Weak transcription	Brain Angular Gyrus	brain
43	chr12:42486000-42513000	Weak transcription	Aorta	Aorta
44	chr12:42486200-42493800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:42486400-42492800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:42486400-42492800	Weak transcription	Left Ventricle	heart
47	chr12:42487000-42496800	Weak transcription	Colonic Mucosa	Colon
48	chr12:42487400-42490600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:42487600-42490600	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr12:42487600-42491000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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