Variant report

Variant	rs277986
Chromosome Location	chr5:70917895-70917896
allele	A/C/G/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	MAX	chr5:70917640-70918014	Hela-S3	cervix:	n/a	n/a
2	FOS	chr5:70917391-70917956	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:70916502..70919682-chr5:70919779..70922694,4	K562	blood:
2	chr5:70910303..70912801-chr5:70916623..70918691,2	K562	blood:
3	chr5:70881536..70885589-chr5:70916347..70918765,3	MCF-7	breast:
4	chr5:70911415..70915310-chr5:70916318..70918922,4	MCF-7	breast:

Variant related genes	Relation type
MCCC2	TF binding region
ENSG00000265613	Chromatin interaction
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:144)

rs_ID	r²[population]
rs10942466	0.81[AMR][1000 genomes]
rs10942683	0.88[AMR][1000 genomes]
rs11742923	0.81[AMR][1000 genomes]
rs12110291	0.85[AMR][1000 genomes]
rs13158264	0.82[AMR][1000 genomes]
rs13175174	0.81[AMR][1000 genomes]
rs13185319	0.82[AMR][1000 genomes]
rs13185743	0.85[AMR][1000 genomes]
rs1559260	0.81[AMR][1000 genomes]
rs156754	0.84[AMR][1000 genomes]
rs156755	0.84[AMR][1000 genomes]
rs157044	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs157045	0.82[AMR][1000 genomes]
rs157046	0.86[AMR][1000 genomes]
rs157049	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1693895	0.86[AMR][1000 genomes]
rs1698063	0.87[AMR][1000 genomes]
rs172148	0.82[AMR][1000 genomes]
rs175872	0.83[AMR][1000 genomes]
rs182190	0.89[AMR][1000 genomes]
rs1833856	0.86[AMR][1000 genomes]
rs185733	0.86[AMR][1000 genomes]
rs188059	0.82[AMR][1000 genomes]
rs190692	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1961760	0.80[AMR][1000 genomes]
rs2059193	0.85[AMR][1000 genomes]
rs2059195	0.81[AMR][1000 genomes]
rs2432059	0.81[AMR][1000 genomes]
rs2432060	0.81[AMR][1000 genomes]
rs2454086	0.81[AMR][1000 genomes]
rs2646639	0.85[AMR][1000 genomes]
rs276590	0.84[AMR][1000 genomes]
rs276591	0.84[AMR][1000 genomes]
rs276592	0.82[AMR][1000 genomes]
rs276594	0.81[AMR][1000 genomes]
rs276597	0.88[AMR][1000 genomes]
rs276598	0.87[AMR][1000 genomes]
rs276599	0.81[AMR][1000 genomes]
rs276600	0.89[AMR][1000 genomes]
rs276601	0.88[AMR][1000 genomes]
rs277936	0.82[EUR][1000 genomes]
rs277939	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs277940	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs277942	0.85[AMR][1000 genomes]
rs277944	0.85[AMR][1000 genomes]
rs277945	0.86[AMR][1000 genomes]
rs277948	0.81[AMR][1000 genomes]
rs277954	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277957	0.86[AMR][1000 genomes]
rs277958	0.86[AMR][1000 genomes]
rs277960	0.86[AMR][1000 genomes]
rs277961	0.82[AMR][1000 genomes]
rs277962	0.86[AMR][1000 genomes]
rs277963	0.86[AMR][1000 genomes]
rs277964	0.86[AMR][1000 genomes]
rs277965	0.86[AMR][1000 genomes]
rs277966	0.85[AMR][1000 genomes]
rs277967	0.83[AMR][1000 genomes]
rs277976	0.83[EUR][1000 genomes]
rs277978	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277979	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277980	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277981	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs277985	0.89[ASN][1000 genomes]
rs277996	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs277999	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278000	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs278001	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs279290	0.84[AMR][1000 genomes]
rs279291	0.89[AMR][1000 genomes]
rs279322	0.83[AMR][1000 genomes]
rs279337	0.86[AMR][1000 genomes]
rs35327154	0.86[AMR][1000 genomes]
rs35420270	0.81[AMR][1000 genomes]
rs36036841	0.87[AMR][1000 genomes]
rs3761965	0.87[AMR][1000 genomes]
rs3761967	0.81[AMR][1000 genomes]
rs378585	0.86[AMR][1000 genomes]
rs384732	0.85[AMR][1000 genomes]
rs3890749	0.87[AMR][1000 genomes]
rs392791	0.85[AMR][1000 genomes]
rs404692	0.84[AMR][1000 genomes]
rs410776	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs418738	0.87[AMR][1000 genomes]
rs4337836	0.81[AMR][1000 genomes]
rs439698	0.81[AMR][1000 genomes]
rs441691	0.81[AMR][1000 genomes]
rs445771	0.81[AMR][1000 genomes]
rs451229	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs457908	0.86[AMR][1000 genomes]
rs458009	0.86[AMR][1000 genomes]
rs458150	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs458370	0.86[AMR][1000 genomes]
rs459298	0.86[AMR][1000 genomes]
rs459787	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs460778	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs461215	0.86[AMR][1000 genomes]
rs462282	0.86[AMR][1000 genomes]
rs463871	0.86[AMR][1000 genomes]
rs464155	0.82[AMR][1000 genomes]
rs464182	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs464594	0.86[AMR][1000 genomes]
rs464962	0.86[AMR][1000 genomes]
rs465073	0.86[AMR][1000 genomes]
rs466930	0.86[AMR][1000 genomes]
rs467160	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs467381	0.82[AMR][1000 genomes]
rs467413	0.86[AMR][1000 genomes]
rs467563	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs467620	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs467851	0.86[AMR][1000 genomes]
rs467901	0.81[AMR][1000 genomes]
rs468028	0.86[AMR][1000 genomes]
rs468033	0.86[AMR][1000 genomes]
rs468128	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs468158	0.86[AMR][1000 genomes]
rs468446	0.86[AMR][1000 genomes]
rs468467	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs468564	0.86[AMR][1000 genomes]
rs468633	0.86[AMR][1000 genomes]
rs468658	0.86[AMR][1000 genomes]
rs468776	0.86[AMR][1000 genomes]
rs468832	0.86[AMR][1000 genomes]
rs469039	0.86[AMR][1000 genomes]
rs469369	0.86[AMR][1000 genomes]
rs469379	0.82[AMR][1000 genomes]
rs469548	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs469617	0.83[AMR][1000 genomes]
rs4704049	0.81[AMR][1000 genomes]
rs4704096	0.86[AMR][1000 genomes]
rs541035	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs544779	0.82[EUR][1000 genomes]
rs560394	0.81[AMR][1000 genomes]
rs62361813	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6871754	0.81[AMR][1000 genomes]
rs6885523	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715748	0.81[AMR][1000 genomes]
rs7443763	0.85[AMR][1000 genomes]
rs7444320	0.82[AMR][1000 genomes]
rs7447146	0.83[AMR][1000 genomes]
rs7702940	0.81[AMR][1000 genomes]
rs7726336	0.81[AMR][1000 genomes]
rs7737101	0.81[AMR][1000 genomes]
rs9791120	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs277986	BDP1	Cis_1M	lymphoblastoid	RTeQTL
rs277986	RP11-195E2.1	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
2	chr5:70893600-70930200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
4	chr5:70897000-70925800	Weak transcription	Right Ventricle	heart
5	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
6	chr5:70897400-70921000	Weak transcription	Fetal Heart	heart
7	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
9	chr5:70898200-70944200	Weak transcription	Osteobl	bone
10	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
11	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:70898600-70922400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
14	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:70900200-70925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:70900200-70928200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:70900200-70930800	Weak transcription	HMEC	breast
18	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:70900400-70922800	Weak transcription	Fetal Kidney	kidney
20	chr5:70900400-70927000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:70900400-70927600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:70900400-70927800	Weak transcription	Brain Substantia Nigra	brain
23	chr5:70900400-70931000	Weak transcription	K562	blood
24	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:70905800-70920200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:70906400-70919600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr5:70906600-70923400	Strong transcription	Primary T cells from cord blood	blood
28	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
29	chr5:70906800-70923400	Strong transcription	Liver	Liver
30	chr5:70907200-70927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr5:70907200-70928200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:70907400-70932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr5:70907600-70928000	Weak transcription	Fetal Lung	lung
34	chr5:70908800-70927200	Weak transcription	Thymus	Thymus
35	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr5:70909200-70931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:70911000-70920200	Strong transcription	Dnd41	blood
38	chr5:70911200-70928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:70912000-70919200	Weak transcription	HSMMtube	muscle
40	chr5:70912200-70931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:70912400-70922800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:70912400-70927000	Weak transcription	Brain Angular Gyrus	brain
43	chr5:70912400-70936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr5:70912600-70927800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
46	chr5:70912600-70943800	Weak transcription	A549	lung
47	chr5:70912800-70918800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:70912800-70919000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr5:70912800-70922800	Weak transcription	HSMM	muscle
50	chr5:70912800-70927000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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