Variant report

Variant	rs4279586
Chromosome Location	chr8:63926591-63926592
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:63925216..63928918-chr8:63929188..63932470,3	K562	blood:
2	chr8:63925803..63927464-chr8:63930970..63933121,2	K562	blood:
3	chr8:63925295..63930979-chr8:63933165..63939315,7	K562	blood:
4	chr8:63925789..63928059-chr8:63949158..63951177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253121	Chromatin interaction
ENSG00000137563	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10100456	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10106324	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10808728	0.84[EUR][1000 genomes]
rs12115136	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12335094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550400	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12679222	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1455574	0.80[EUR][1000 genomes]
rs2043525	1.00[CHB][hapmap]
rs2353388	0.82[EUR][1000 genomes]
rs2736676	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4352845	0.82[EUR][1000 genomes]
rs4377959	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4397399	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4400383	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4413770	0.82[EUR][1000 genomes]
rs4446729	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4449783	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4573267	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4592024	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4739049	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs5007413	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6472066	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6998134	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6998383	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6999604	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7000012	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7003413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7010484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016339	1.00[CHB][hapmap]
rs7387326	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7388305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs7818905	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7839216	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7839874	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4279586	CLVS1	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:63920800-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr8:63922000-63932000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr8:63922200-63935600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr8:63922400-63941800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr8:63922600-63936600	Weak transcription	HSMM	muscle
6	chr8:63922600-63949200	Weak transcription	Fetal Brain Female	brain
7	chr8:63922800-63928600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:63922800-63931000	Weak transcription	Thymus	Thymus
9	chr8:63922800-63937600	Weak transcription	Fetal Thymus	thymus
10	chr8:63922800-63938000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr8:63922800-63938000	Weak transcription	Esophagus	oesophagus
12	chr8:63922800-63939200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:63922800-63941000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr8:63922800-63950000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr8:63922800-63950000	Weak transcription	HMEC	breast
16	chr8:63922800-63950800	Weak transcription	Fetal Muscle Leg	muscle
17	chr8:63923000-63926600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:63923200-63930400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr8:63923400-63940800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:63923600-63941800	Weak transcription	Brain Hippocampus Middle	brain
21	chr8:63923600-63944600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr8:63923800-63950600	Weak transcription	Fetal Kidney	kidney
23	chr8:63924000-63928200	Weak transcription	HepG2	liver
24	chr8:63924000-63944800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr8:63924200-63935600	Weak transcription	GM12878-XiMat	blood
26	chr8:63924200-63941200	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr8:63924200-63941800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr8:63924400-63937600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr8:63924800-63933800	Weak transcription	HUVEC	blood vessel
30	chr8:63924800-63935600	Weak transcription	Fetal Intestine Large	intestine
31	chr8:63924800-63941000	Weak transcription	Fetal Intestine Small	intestine
32	chr8:63925800-63927000	Strong transcription	Liver	Liver
33	chr8:63925800-63929000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:63926000-63937400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr8:63926200-63926800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr8:63926200-63927000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr8:63926200-63945200	Weak transcription	A549	lung
38	chr8:63926200-63949000	Weak transcription	Brain Germinal Matrix	brain
39	chr8:63926200-63949400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr8:63926400-63936800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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