Variant report

Variant	rs11799413
Chromosome Location	chr1:227270914-227270915
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	SETDB1	chr1:227270891-227271628	U2OS	brain:	n/a	n/a
2	KAP1	chr1:227270894-227271092	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227270688..227272597-chr1:227288564..227290914,2	MCF-7	breast:

Variant related genes	Relation type
CDC42BPA	TF binding region
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1015815	0.86[AMR][1000 genomes]
rs1015816	0.80[AMR][1000 genomes]
rs10495258	0.96[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs10495266	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10495269	0.96[EUR][1000 genomes]
rs10495270	0.96[EUR][1000 genomes]
rs10916109	0.83[AMR][1000 genomes]
rs11800062	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11801443	0.98[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11802395	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11803959	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11805298	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11806820	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11807094	0.96[YRI][hapmap]
rs11808186	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11808962	0.96[YRI][hapmap]
rs11809998	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11810328	0.83[AMR][1000 genomes]
rs12401556	0.96[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403195	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12403833	0.89[CEU][hapmap];0.96[EUR][1000 genomes]
rs12404494	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12404627	0.96[EUR][1000 genomes]
rs12405122	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12405707	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12405723	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12407061	0.96[EUR][1000 genomes]
rs12407545	0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12408437	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12409816	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap]
rs12410337	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12411017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1320493	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes]
rs1513600	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1513602	0.83[AMR][1000 genomes]
rs1513603	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1546557	0.83[AMR][1000 genomes]
rs16846855	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16846874	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846877	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846908	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846910	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846911	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs16847492	1.00[CEU][hapmap]
rs17605533	0.96[EUR][1000 genomes]
rs17851754	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1888830	0.82[AFR][1000 genomes]
rs1888831	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2090009	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2150869	0.93[EUR][1000 genomes]
rs2150871	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2150873	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2183837	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34400564	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34953255	0.96[EUR][1000 genomes]
rs41303115	0.94[EUR][1000 genomes]
rs4354510	0.83[AMR][1000 genomes]
rs4551563	0.96[EUR][1000 genomes]
rs55685166	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55865118	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55946024	0.83[AMR][1000 genomes]
rs56834719	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57513303	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58489467	0.83[AMR][1000 genomes]
rs58532064	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59116340	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59859849	0.83[AMR][1000 genomes]
rs60079575	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60291100	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60641481	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60866629	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60979561	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61522132	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6659506	0.83[AMR][1000 genomes]
rs6675383	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6696791	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6696794	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6701743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73086746	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086752	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73086775	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73088658	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73089725	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73089746	0.83[AFR][1000 genomes]
rs73089747	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73089755	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73089760	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73089765	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73089770	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73090612	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73091738	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091740	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091742	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091755	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091757	0.83[AFR][1000 genomes]
rs73091759	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091761	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73091766	0.83[AFR][1000 genomes]
rs73091774	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73093463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093467	0.82[AFR][1000 genomes]
rs73093495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73096350	0.83[AMR][1000 genomes]
rs73096353	0.83[AMR][1000 genomes]
rs73096358	0.83[AMR][1000 genomes]
rs73096883	0.81[AFR][1000 genomes]
rs73099023	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73099026	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73100804	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73100814	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73100852	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73102915	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73102920	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102930	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102936	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7413768	0.94[EUR][1000 genomes]
rs74140276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140278	0.83[AFR][1000 genomes]
rs74140289	0.81[AFR][1000 genomes]
rs74143321	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7515739	0.83[AMR][1000 genomes]
rs7526283	1.00[CEU][hapmap]
rs7534286	0.81[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs7539037	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7539750	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap]
rs7545775	0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1012482	chr1:227212024-227271750	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv998420	chr1:227228591-227275031	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227178400-227271200	Weak transcription	Psoas Muscle	Psoas
3	chr1:227190600-227272600	Weak transcription	Lung	lung
4	chr1:227203000-227278800	Weak transcription	Pancreas	Pancrea
5	chr1:227209000-227272400	Weak transcription	Fetal Intestine Small	intestine
6	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
8	chr1:227216800-227287600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:227217000-227271400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227217000-227278800	Weak transcription	Placenta	Placenta
11	chr1:227220600-227272600	Weak transcription	Aorta	Aorta
12	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
13	chr1:227226800-227272400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:227226800-227278400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:227226800-227285600	Weak transcription	Brain Germinal Matrix	brain
16	chr1:227227000-227272200	Weak transcription	Fetal Heart	heart
17	chr1:227227000-227282200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:227227400-227272400	Weak transcription	Ovary	ovary
19	chr1:227227400-227281200	Weak transcription	Fetal Kidney	kidney
20	chr1:227227400-227284200	Weak transcription	Brain Angular Gyrus	brain
21	chr1:227228000-227277000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:227232800-227279200	Weak transcription	Stomach Mucosa	stomach
23	chr1:227235800-227271000	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:227236000-227286200	Weak transcription	Fetal Brain Male	brain
25	chr1:227238600-227278400	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:227239800-227271200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr1:227239800-227271400	Weak transcription	Fetal Intestine Large	intestine
28	chr1:227240000-227286800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:227246400-227278400	Weak transcription	NH-A	brain
30	chr1:227247400-227272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:227247400-227299800	Weak transcription	HMEC	breast
32	chr1:227248800-227271200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:227249800-227271200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:227253600-227278600	Weak transcription	Adipose Nuclei	Adipose
36	chr1:227254000-227271600	Weak transcription	Left Ventricle	heart
37	chr1:227254000-227272000	Weak transcription	Fetal Stomach	stomach
38	chr1:227255000-227271800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:227257000-227278400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr1:227257600-227288000	Weak transcription	HSMMtube	muscle
41	chr1:227257800-227271000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:227259000-227280600	Weak transcription	HepG2	liver
44	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
45	chr1:227259600-227271400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:227260000-227278600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr1:227260200-227278600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:227260200-227281800	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:227260400-227287800	Weak transcription	NHEK	skin
50	chr1:227260600-227271400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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