Variant report

Variant	rs11545078
Chromosome Location	chr8:63938764-63938765
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	chr8:63937516..63940331-chr8:63949992..63952545,2	K562	blood:
2	chr8:63925295..63930979-chr8:63933165..63939315,7	K562	blood:

Variant related genes	Relation type
ENSG00000240915	Chromatin interaction
ENSG00000137563	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10504360	0.93[ASN][1000 genomes]
rs10504361	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11985884	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11985904	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11989852	0.89[GIH][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11990678	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11992253	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11993022	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16929879	0.82[ASN][1000 genomes]
rs16930045	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930060	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16930066	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16930072	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17192653	0.93[ASN][1000 genomes]
rs17194931	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279355	0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279558	0.96[GIH][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902232	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902233	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1902234	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1902235	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124294	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2353363	0.98[ASN][1000 genomes]
rs2353364	0.98[ASN][1000 genomes]
rs28387373	0.82[ASN][1000 genomes]
rs2883148	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780127	0.96[GIH][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780129	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4395892	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4410897	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4419801	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55800505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034470	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213868	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56339102	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57069084	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57776226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58942648	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59169978	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60751452	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60889737	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60897253	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61326296	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61518338	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61629446	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508064	0.82[ASN][1000 genomes]
rs62508088	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508107	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508108	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508109	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508110	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62508111	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508113	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508123	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508154	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508155	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508156	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62508157	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62508158	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510060	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510061	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510062	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510063	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62510064	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6472063	0.95[ASN][1000 genomes]
rs66790008	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983219	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6983643	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983864	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6983896	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6997520	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7015120	0.81[ASN][1000 genomes]
rs7015302	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72656550	0.93[ASN][1000 genomes]
rs72658344	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72658396	0.98[ASN][1000 genomes]
rs72658400	0.98[ASN][1000 genomes]
rs72659813	0.95[ASN][1000 genomes]
rs7834301	0.95[ASN][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	nsv1033527	chr8:63673915-64073735	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11545078	GGH	cis	Artery Tibial	GTEx
rs11545078	GGH	cis	Nerve Tibial	GTEx
rs11545078	GGH	Cis_1M	lymphoblastoid	RTeQTL
rs11545078	GGH	cis	Skin Sun Exposed Lower leg	GTEx
rs11545078	GGH	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63922400-63941800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr8:63922600-63949200	Weak transcription	Fetal Brain Female	brain
3	chr8:63922800-63939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr8:63922800-63941000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:63922800-63950000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:63922800-63950000	Weak transcription	HMEC	breast
7	chr8:63922800-63950800	Weak transcription	Fetal Muscle Leg	muscle
8	chr8:63923400-63940800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr8:63923600-63941800	Weak transcription	Brain Hippocampus Middle	brain
10	chr8:63923600-63944600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr8:63923800-63950600	Weak transcription	Fetal Kidney	kidney
12	chr8:63924000-63944800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr8:63924200-63941200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr8:63924200-63941800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr8:63924800-63941000	Weak transcription	Fetal Intestine Small	intestine
16	chr8:63926200-63945200	Weak transcription	A549	lung
17	chr8:63926200-63949000	Weak transcription	Brain Germinal Matrix	brain
18	chr8:63926200-63949400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:63927000-63939800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr8:63929200-63949200	Weak transcription	Fetal Brain Male	brain
21	chr8:63929400-63945400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr8:63931400-63950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:63932200-63942800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr8:63932600-63940200	Weak transcription	Primary B cells from cord blood	blood
25	chr8:63935400-63939600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr8:63935400-63949200	Weak transcription	K562	blood
27	chr8:63935800-63950000	Weak transcription	NHDF-Ad	bronchial
28	chr8:63936200-63941000	Weak transcription	Fetal Intestine Large	intestine
29	chr8:63936200-63949600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr8:63936400-63948800	Weak transcription	GM12878-XiMat	blood
31	chr8:63936400-63949400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr8:63936800-63949800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr8:63936800-63949800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr8:63937000-63938800	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr8:63937000-63939200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr8:63937000-63940600	Weak transcription	HepG2	liver
37	chr8:63937200-63941000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr8:63937600-63938800	Weak transcription	Osteobl	bone
39	chr8:63937800-63939200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr8:63938000-63938800	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr8:63938000-63938800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr8:63938000-63940800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr8:63938000-63940800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr8:63938000-63941000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr8:63938000-63949200	Weak transcription	NHEK	skin
46	chr8:63938000-63950000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr8:63938200-63943200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr8:63938200-63950600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr8:63938400-63939000	Enhancers	Fetal Heart	heart
50	chr8:63938600-63939200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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