Variant report

Variant	rs12541873
Chromosome Location	chr8:63935457-63935458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:63932030..63935472-chr8:63949746..63951856,3	K562	blood:
2	chr8:63935416..63938127-chr8:63942225..63943777,2	K562	blood:
3	chr8:63925295..63930979-chr8:63933165..63939315,7	K562	blood:

Variant related genes	Relation type
ENSG00000137563	Chromatin interaction
ENSG00000240915	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1031553	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10957259	0.82[EUR][1000 genomes]
rs10957262	0.82[EUR][1000 genomes]
rs10957263	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10957264	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10957267	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11994355	0.82[EUR][1000 genomes]
rs12541798	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12544234	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12548933	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12681818	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12681874	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16918945	0.82[EUR][1000 genomes]
rs16918948	0.82[EUR][1000 genomes]
rs16930047	0.84[EUR][1000 genomes]
rs16930051	0.82[EUR][1000 genomes]
rs16930062	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16930070	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124293	0.84[EUR][1000 genomes]
rs2168316	0.84[EUR][1000 genomes]
rs2168317	0.84[EUR][1000 genomes]
rs4534127	0.87[ASN][1000 genomes]
rs4581048	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737623	0.82[EUR][1000 genomes]
rs4739033	0.84[EUR][1000 genomes]
rs4739034	0.84[EUR][1000 genomes]
rs4739039	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4739040	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4739041	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57646286	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57863684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59202889	0.84[EUR][1000 genomes]
rs60408006	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60782904	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60800990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60865954	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62508118	0.84[EUR][1000 genomes]
rs62508120	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62508122	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62510065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6984196	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7004312	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7017200	0.85[EUR][1000 genomes];0.95[ASN][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	nsv1018879	chr8:63281724-63937632	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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
3	nsv6227	chr8:63892087-63936952	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12541873	GGH	cis	Artery Tibial	GTEx
rs12541873	GGH	cis	lung	GTEx
rs12541873	GGH	cis	Nerve Tibial	GTEx
rs12541873	GGH	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63920800-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:63922200-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:63922400-63941800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr8:63922600-63936600	Weak transcription	HSMM	muscle
5	chr8:63922600-63949200	Weak transcription	Fetal Brain Female	brain
6	chr8:63922800-63937600	Weak transcription	Fetal Thymus	thymus
7	chr8:63922800-63938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:63922800-63938000	Weak transcription	Esophagus	oesophagus
9	chr8:63922800-63939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:63922800-63941000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:63922800-63950000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr8:63922800-63950000	Weak transcription	HMEC	breast
13	chr8:63922800-63950800	Weak transcription	Fetal Muscle Leg	muscle
14	chr8:63923400-63940800	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr8:63923600-63941800	Weak transcription	Brain Hippocampus Middle	brain
16	chr8:63923600-63944600	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr8:63923800-63950600	Weak transcription	Fetal Kidney	kidney
18	chr8:63924000-63944800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr8:63924200-63935600	Weak transcription	GM12878-XiMat	blood
20	chr8:63924200-63941200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:63924200-63941800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr8:63924400-63937600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr8:63924800-63935600	Weak transcription	Fetal Intestine Large	intestine
24	chr8:63924800-63941000	Weak transcription	Fetal Intestine Small	intestine
25	chr8:63926000-63937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr8:63926200-63945200	Weak transcription	A549	lung
27	chr8:63926200-63949000	Weak transcription	Brain Germinal Matrix	brain
28	chr8:63926200-63949400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr8:63926400-63936800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr8:63927000-63939800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr8:63928600-63936000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:63929000-63937000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr8:63929200-63949200	Weak transcription	Fetal Brain Male	brain
34	chr8:63929400-63945400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr8:63929600-63936000	Weak transcription	HepG2	liver
36	chr8:63929600-63937400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr8:63929800-63935600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:63930200-63935600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr8:63931200-63936200	Weak transcription	Thymus	Thymus
40	chr8:63931400-63936600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr8:63931400-63950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr8:63932200-63942800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr8:63932600-63940200	Weak transcription	Primary B cells from cord blood	blood
44	chr8:63933000-63936400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr8:63933800-63935600	Weak transcription	Liver	Liver
46	chr8:63933800-63936800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr8:63934000-63936800	Weak transcription	NH-A	brain
48	chr8:63934200-63935800	Weak transcription	HUVEC	blood vessel
49	chr8:63934400-63936800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr8:63934400-63937600	Weak transcription	NHEK	skin

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