Variant report

Variant	rs1469338
Chromosome Location	chr8:59357456-59357457
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:59323727..59326443-chr8:59354351..59357969,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215114	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10095270	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100741	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs10105913	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10108817	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10110824	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10111761	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11552203	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13251671	0.94[ASN][1000 genomes]
rs13252159	0.88[ASN][1000 genomes]
rs13255706	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap]
rs13271316	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13271916	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274906	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs13277110	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17202769	0.94[ASN][1000 genomes]
rs17202790	0.94[ASN][1000 genomes]
rs17261333	0.81[ASN][1000 genomes]
rs17261550	1.00[CHB][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35476562	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4599797	1.00[CEU][hapmap];0.92[GIH][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67257878	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv890938	chr8:59355053-59809785	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1469338	CLVS1	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:59324800-59362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr8:59325000-59357600	Weak transcription	NHLF	lung
3	chr8:59325000-59360000	Weak transcription	Right Ventricle	heart
4	chr8:59325000-59361200	Weak transcription	Psoas Muscle	Psoas
5	chr8:59325200-59370800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr8:59325800-59363200	Weak transcription	Hela-S3	cervix
7	chr8:59326600-59361400	Weak transcription	Fetal Brain Male	brain
8	chr8:59326600-59366200	Weak transcription	Gastric	stomach
9	chr8:59332600-59364800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:59334400-59364200	Weak transcription	HMEC	breast
11	chr8:59336000-59361400	Weak transcription	Spleen	Spleen
12	chr8:59336000-59364800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr8:59336000-59366600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr8:59336600-59360800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr8:59337800-59363200	Weak transcription	Pancreas	Pancrea
16	chr8:59339600-59363400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr8:59342200-59366200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr8:59342400-59365400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr8:59343600-59357600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr8:59349600-59361600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr8:59349800-59370800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr8:59351600-59362400	Weak transcription	Fetal Stomach	stomach
23	chr8:59353400-59361000	Weak transcription	Placenta	Placenta
24	chr8:59353400-59364600	Weak transcription	Brain Anterior Caudate	brain
25	chr8:59353600-59362200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr8:59353800-59361000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr8:59353800-59370400	Weak transcription	Esophagus	oesophagus
28	chr8:59354000-59358400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr8:59354600-59364200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr8:59354800-59357600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr8:59354800-59357800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:59354800-59358400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:59354800-59359400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr8:59354800-59359400	Weak transcription	Fetal Intestine Small	intestine
35	chr8:59354800-59359600	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:59354800-59360000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr8:59354800-59360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr8:59354800-59360000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr8:59354800-59360000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr8:59354800-59360000	Weak transcription	GM12878-XiMat	blood
41	chr8:59354800-59360200	Weak transcription	Dnd41	blood
42	chr8:59354800-59360400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr8:59354800-59360600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr8:59354800-59360800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr8:59354800-59360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr8:59354800-59360800	Weak transcription	Aorta	Aorta
47	chr8:59354800-59360800	Weak transcription	Fetal Brain Female	brain
48	chr8:59354800-59360800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr8:59354800-59360800	Weak transcription	Left Ventricle	heart
50	chr8:59354800-59360800	Weak transcription	Ovary	ovary

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