Variant report

Variant	rs6665512
Chromosome Location	chr1:227762808-227762809
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	chr1:227750097..227752403-chr1:227761734..227764145,2	K562	blood:
2	chr1:227751959..227755569-chr1:227762720..227764448,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs12563117	1.00[EUR][1000 genomes]
rs12563564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564736	1.00[EUR][1000 genomes]
rs12564917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564929	1.00[EUR][1000 genomes]
rs12565099	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12565109	1.00[EUR][1000 genomes]
rs12565618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566716	1.00[EUR][1000 genomes]
rs12567084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567934	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1323021	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13373816	1.00[EUR][1000 genomes]
rs16841323	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847822	1.00[AMR][1000 genomes]
rs16847912	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847926	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847929	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847948	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848026	1.00[EUR][1000 genomes]
rs16848044	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16859962	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17492440	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17492447	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2313220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34984248	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35703429	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4462138	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57165550	1.00[AMR][1000 genomes]
rs58322371	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58961542	0.94[ASN][1000 genomes]
rs59404931	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59461077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59772630	1.00[AMR][1000 genomes]
rs60835672	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61283390	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6675470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73088936	1.00[AMR][1000 genomes]
rs73090912	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090935	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090942	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090947	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73090948	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090952	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090954	1.00[ASN][1000 genomes]
rs73090959	1.00[AMR][1000 genomes]
rs73090985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73090995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73091000	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73092646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092653	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73092665	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73093304	1.00[AMR][1000 genomes]
rs73093319	1.00[AMR][1000 genomes]
rs73093328	1.00[AMR][1000 genomes]
rs73093344	1.00[AMR][1000 genomes]
rs73093354	1.00[AMR][1000 genomes]
rs73094528	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094538	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094556	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094558	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094561	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73094566	0.95[AFR][1000 genomes]
rs73094571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099300	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73099302	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73101625	1.00[AMR][1000 genomes]
rs73101653	1.00[AMR][1000 genomes]
rs73102372	1.00[AMR][1000 genomes]
rs73102384	1.00[AMR][1000 genomes]
rs73102391	1.00[AMR][1000 genomes]
rs73104364	1.00[AMR][1000 genomes]
rs7526436	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7533013	0.87[ASN][1000 genomes]
rs7546845	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7554851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554870	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7555208	1.00[AMR][1000 genomes]
rs996226	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3338615	chr1:227738421-227798486	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	esv3327012	chr1:227741102-227890968	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227752000-227766800	Weak transcription	Ovary	ovary
2	chr1:227752200-227763200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:227752200-227774400	Weak transcription	Aorta	Aorta
4	chr1:227752400-227763000	Weak transcription	Stomach Mucosa	stomach
5	chr1:227752400-227763800	Weak transcription	HSMMtube	muscle
6	chr1:227752400-227766800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:227752400-227780600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:227753600-227763000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:227754400-227783600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:227760200-227773600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:227760200-227783800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227760200-227784600	Weak transcription	Fetal Kidney	kidney
13	chr1:227760400-227765400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:227760400-227767000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:227760800-227763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:227760800-227766800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:227760800-227766800	Weak transcription	Esophagus	oesophagus
18	chr1:227760800-227766800	Weak transcription	Fetal Stomach	stomach
19	chr1:227760800-227766800	Weak transcription	Left Ventricle	heart
20	chr1:227760800-227766800	Weak transcription	Lung	lung
21	chr1:227760800-227766800	Weak transcription	Pancreas	Pancrea
22	chr1:227760800-227766800	Weak transcription	Right Ventricle	heart
23	chr1:227760800-227766800	Weak transcription	Spleen	Spleen
24	chr1:227760800-227767000	Weak transcription	Gastric	stomach
25	chr1:227760800-227767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:227760800-227767200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:227760800-227772800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:227761000-227767000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr1:227761600-227763600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr1:227762800-227763000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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