Variant report

Variant	rs12090220
Chromosome Location	chr1:170042254-170042255
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:170042163-170044116	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:170032663..170035514-chr1:170040847..170042460,2	MCF-7	breast:
2	chr1:170037046..170038634-chr1:170041259..170042880,2	K562	blood:

Variant related genes	Relation type
KIFAP3	TF binding region
ENSG00000075945	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10158922	1.00[AMR][1000 genomes]
rs10218486	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919276	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919288	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919294	0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919295	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919296	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10919300	1.00[EUR][1000 genomes]
rs10919308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12025296	1.00[EUR][1000 genomes]
rs12044536	1.00[EUR][1000 genomes]
rs12061373	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12061500	1.00[AMR][1000 genomes]
rs12061626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12066551	1.00[EUR][1000 genomes]
rs12071325	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073288	1.00[EUR][1000 genomes]
rs12075569	1.00[EUR][1000 genomes]
rs12076018	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12077708	1.00[EUR][1000 genomes]
rs12079608	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12084420	1.00[AMR][1000 genomes]
rs12087450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12088186	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12091389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095784	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16862886	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16862978	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2103641	1.00[EUR][1000 genomes]
rs2272912	1.00[EUR][1000 genomes]
rs2901261	1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4279900	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57038529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73023593	1.00[EUR][1000 genomes]
rs73041148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73041149	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122312	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74122452	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7531947	1.00[EUR][1000 genomes]
rs989054	1.00[AMR][1000 genomes];1.00[EUR][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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169952400-170043000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:170018200-170042400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:170019000-170042600	Weak transcription	Thymus	Thymus
4	chr1:170019200-170042400	Weak transcription	Fetal Lung	lung
5	chr1:170032800-170042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:170032800-170042600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:170033800-170042400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:170036600-170043000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr1:170036800-170042600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:170037000-170042600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr1:170037000-170042800	Weak transcription	Right Atrium	heart
12	chr1:170037000-170043000	Weak transcription	Left Ventricle	heart
13	chr1:170037000-170043200	Weak transcription	Small Intestine	intestine
14	chr1:170037200-170042600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:170037200-170042600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:170037200-170042600	Weak transcription	Fetal Thymus	thymus
17	chr1:170037200-170042600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr1:170037200-170042600	Weak transcription	HepG2	liver
19	chr1:170037200-170043200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:170037400-170043000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr1:170037800-170042600	Weak transcription	Fetal Heart	heart
22	chr1:170038000-170043200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:170038600-170042600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:170038600-170043000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:170038600-170043000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:170039400-170042600	Weak transcription	Fetal Stomach	stomach
27	chr1:170040000-170042600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:170040000-170043000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:170040600-170042400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:170040800-170042400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:170040800-170042600	Enhancers	Fetal Brain Male	brain
32	chr1:170041000-170042400	Weak transcription	Brain Germinal Matrix	brain
33	chr1:170041000-170042600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:170041000-170042600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr1:170041000-170042600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:170041000-170042600	Weak transcription	Aorta	Aorta
37	chr1:170041000-170042600	Weak transcription	Fetal Muscle Leg	muscle
38	chr1:170041000-170043000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:170041000-170043200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:170041000-170044200	Active TSS	GM12878-XiMat	blood
41	chr1:170041200-170042600	Weak transcription	Liver	Liver
42	chr1:170041200-170043000	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:170041400-170042400	Weak transcription	Primary T cells from cord blood	blood
44	chr1:170041400-170042400	Enhancers	Brain Hippocampus Middle	brain
45	chr1:170041400-170042600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:170041400-170042600	Enhancers	Brain Anterior Caudate	brain
47	chr1:170041400-170043000	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr1:170041400-170043400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:170041400-170044200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr1:170041600-170042600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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