Variant report

Variant	rs4951476
Chromosome Location	chr1:213224719-213224720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213187916..213191474-chr1:213223097..213226356,5	K562	blood:
2	chr1:213188825..213190728-chr1:213222994..213225299,2	MCF-7	breast:
3	chr1:213187916..213189691-chr1:213222882..213226054,4	K562	blood:
4	chr1:213184074..213185993-chr1:213223690..213226218,2	K562	blood:

Variant related genes	Relation type
ENSG00000174606	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10127851	0.84[EUR][1000 genomes]
rs10465694	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10864034	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10864036	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11120082	0.84[EUR][1000 genomes]
rs1566247	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1566248	0.82[EUR][1000 genomes]
rs1976333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995151	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2132428	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2172982	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2173398	0.84[EUR][1000 genomes]
rs2494767	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2817976	0.82[EUR][1000 genomes]
rs2817984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2935209	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2935219	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936010	0.82[EUR][1000 genomes]
rs2936011	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002285	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3010779	1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3010780	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.83[ASN][1000 genomes]
rs3010787	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3010789	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3124668	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4543872	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4951475	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4951478	0.81[EUR][1000 genomes]
rs4951479	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4951662	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951677	0.84[EUR][1000 genomes]
rs6540774	0.83[EUR][1000 genomes]
rs6540776	0.82[EUR][1000 genomes]
rs6540778	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540780	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6540781	0.88[EUR][1000 genomes]
rs6540782	0.84[EUR][1000 genomes]
rs6657234	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs6658259	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6666814	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6670025	0.88[ASN][1000 genomes]
rs6671872	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[EUR][1000 genomes]
rs6679510	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6691488	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6692056	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6692144	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6693291	0.82[EUR][1000 genomes]
rs6697921	0.82[EUR][1000 genomes]
rs6699158	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6700169	0.84[EUR][1000 genomes]
rs7535369	0.84[EUR][1000 genomes]
rs7547274	0.84[EUR][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	nsv1008594	chr1:213110654-213236750	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4951476	RPS6KC1	cis	Artery Tibial	GTEx
rs4951476	ANGEL2	cis	Nerve Tibial	GTEx
rs4951476	ANGEL2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213223600-213225200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr1:213223600-213225200	Active TSS	Fetal Lung	lung
3	chr1:213223600-213225200	Active TSS	A549	lung
4	chr1:213223600-213225400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:213223600-213225800	Active TSS	Psoas Muscle	Psoas
6	chr1:213223600-213225800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:213223800-213224800	Active TSS	Primary B cells from cord blood	blood
8	chr1:213223800-213225200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:213223800-213225200	Active TSS	Fetal Kidney	kidney
10	chr1:213223800-213225200	Active TSS	NH-A	brain
11	chr1:213223800-213225400	Active TSS	Rectal Smooth Muscle	rectum
12	chr1:213223800-213225600	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:213223800-213226000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:213224000-213224800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr1:213224000-213225000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
16	chr1:213224000-213225200	Active TSS	Primary T cells from cord blood	blood
17	chr1:213224000-213225200	Active TSS	Fetal Brain Female	brain
18	chr1:213224000-213225200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:213224000-213225200	Active TSS	HMEC	breast
20	chr1:213224000-213225400	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr1:213224000-213225400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:213224000-213225400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:213224000-213225400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:213224000-213225400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:213224000-213225400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:213224000-213225400	Active TSS	Colonic Mucosa	Colon
27	chr1:213224000-213225400	Active TSS	Fetal Muscle Trunk	muscle
28	chr1:213224000-213225400	Active TSS	Left Ventricle	heart
29	chr1:213224000-213225400	Active TSS	Ovary	ovary
30	chr1:213224000-213225600	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr1:213224000-213225600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr1:213224000-213225600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:213224000-213225600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:213224000-213225600	Active TSS	Right Atrium	heart
35	chr1:213224000-213225600	Active TSS	NHDF-Ad	bronchial
36	chr1:213224000-213225800	Flanking Active TSS	Adipose Nuclei	Adipose
37	chr1:213224000-213226400	Active TSS	HSMMtube	muscle
38	chr1:213224200-213225000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr1:213224200-213225000	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr1:213224200-213225000	Active TSS	HepG2	liver
41	chr1:213224200-213225200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:213224200-213225200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:213224200-213225200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:213224200-213225200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:213224200-213225200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:213224200-213225200	Active TSS	Brain Hippocampus Middle	brain
47	chr1:213224200-213225200	Active TSS	Colon Smooth Muscle	Colon
48	chr1:213224200-213225200	Active TSS	Fetal Intestine Small	intestine
49	chr1:213224200-213225200	Active TSS	Fetal Stomach	stomach
50	chr1:213224200-213225200	Active TSS	Lung	lung

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