Variant report

Variant	rs6540780
Chromosome Location	chr1:213300168-213300169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213185297..213187346-chr1:213297966..213300282,2	K562	blood:
2	chr1:213297745..213301905-chr1:213305900..213310308,6	K562	blood:
3	chr1:213299788..213302212-chr1:214389451..214391976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10127851	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10465694	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10864034	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10864036	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10864038	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11120082	0.81[EUR][1000 genomes]
rs1391549	0.87[AMR][1000 genomes]
rs1391550	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1498357	0.89[AMR][1000 genomes]
rs1566247	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1566248	0.83[EUR][1000 genomes]
rs17020338	0.84[AMR][1000 genomes]
rs1976333	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1995151	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2173398	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2494767	0.86[AMR][1000 genomes]
rs2647387	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2817976	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2817978	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2817981	0.89[AMR][1000 genomes]
rs2841427	0.87[AMR][1000 genomes]
rs2841439	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2935219	0.83[AMR][1000 genomes]
rs2936011	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3010779	0.81[AMR][1000 genomes]
rs3010789	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4543872	0.81[AMR][1000 genomes]
rs4655386	0.84[AMR][1000 genomes]
rs4951475	0.82[EUR][1000 genomes]
rs4951476	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4951478	0.82[EUR][1000 genomes]
rs4951479	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4951662	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4951677	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6419470	0.85[AMR][1000 genomes]
rs6540774	0.82[EUR][1000 genomes]
rs6540776	0.83[EUR][1000 genomes]
rs6540778	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540781	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6540782	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6657234	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6658259	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6666814	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6670025	0.82[ASN][1000 genomes]
rs6671872	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6679510	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs6691488	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6692056	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6692144	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6693291	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6697921	0.81[EUR][1000 genomes]
rs6699158	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6700169	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7535369	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7547274	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9308430	0.85[AMR][1000 genomes]
rs9429901	0.84[AMR][1000 genomes]
rs9429902	0.84[AMR][1000 genomes]
rs9430118	0.85[AMR][1000 genomes]
rs9430120	0.83[AMR][1000 genomes]
rs9430121	0.84[AMR][1000 genomes]
rs9430122	0.83[AMR][1000 genomes]
rs9430123	0.86[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392967	chr1:213271844-213490132	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540780	RPS6KC1	cis	Artery Tibial	GTEx
rs6540780	ANGEL2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213261600-213309200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:213261600-213327400	Weak transcription	Aorta	Aorta
3	chr1:213269400-213308400	Weak transcription	Ovary	ovary
4	chr1:213269600-213311800	Weak transcription	Primary B cells from cord blood	blood
5	chr1:213271200-213309200	Weak transcription	Adipose Nuclei	Adipose
6	chr1:213271600-213310200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:213281200-213301000	Weak transcription	Fetal Lung	lung
8	chr1:213281200-213309000	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:213281200-213309400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:213281200-213320400	Weak transcription	Primary T cells from cord blood	blood
11	chr1:213281400-213303400	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr1:213281400-213311000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:213284200-213317200	Weak transcription	Left Ventricle	heart
14	chr1:213284600-213309400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:213284600-213349800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:213285400-213317200	Weak transcription	Fetal Kidney	kidney
17	chr1:213285600-213303000	Weak transcription	GM12878-XiMat	blood
18	chr1:213292400-213317400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:213294000-213310000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr1:213294200-213300600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:213294200-213321400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:213296400-213305400	Weak transcription	Brain Substantia Nigra	brain
23	chr1:213296800-213300400	Weak transcription	Brain Hippocampus Middle	brain
24	chr1:213297200-213305400	Weak transcription	Brain Anterior Caudate	brain
25	chr1:213297400-213305400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:213297400-213308400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:213297400-213320400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:213297600-213300200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:213297600-213300400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:213297600-213300400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:213297600-213300400	Weak transcription	NHDF-Ad	bronchial
32	chr1:213297600-213300400	Weak transcription	NHLF	lung
33	chr1:213297600-213305200	Weak transcription	HepG2	liver
34	chr1:213297600-213309600	Weak transcription	Fetal Intestine Large	intestine
35	chr1:213297600-213313600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:213297800-213300200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:213297800-213300200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:213297800-213300200	Weak transcription	Osteobl	bone
39	chr1:213297800-213300400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:213297800-213300400	Weak transcription	Hela-S3	cervix
41	chr1:213297800-213300400	Weak transcription	HMEC	breast
42	chr1:213297800-213300400	Weak transcription	NHEK	skin
43	chr1:213297800-213300600	Weak transcription	HSMM	muscle
44	chr1:213297800-213305400	Weak transcription	NH-A	brain
45	chr1:213297800-213309200	Weak transcription	Fetal Heart	heart
46	chr1:213297800-213309400	Weak transcription	Fetal Intestine Small	intestine
47	chr1:213297800-213309600	Weak transcription	Gastric	stomach
48	chr1:213297800-213310600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:213298200-213309400	Weak transcription	Psoas Muscle	Psoas
50	chr1:213298600-213300800	Enhancers	K562	blood

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