Variant report

Variant	rs1368408
Chromosome Location	chr5:147258162-147258163
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:147258132-147258182	AG04449	skin:	fetal
2	chr5:147258132-147258182	HRPEpiC	eye:	n/a
3	chr5:147258132-147258182	K562	blood:	n/a
4	chr5:147258132-147258182	HIPEpiC	eye:	n/a
5	chr5:147258132-147258182	AoSMC	blood vessel:	n/a
6	chr5:147258132-147258182	T-47D	breast:	n/a
7	chr5:147258132-147258182	HRE	kidney:	n/a
8	chr5:147258132-147258182	NH-A	brain:	n/a
9	chr5:147258132-147258182	SK-N-SH	brain:	n/a
10	chr5:147258132-147258182	ovcar-3	ovarian:	n/a
11	chr5:147258132-147258182	U87	brain:	n/a
12	chr5:147258132-147258182	AG09319	gingival:	n/a
13	chr5:147258132-147258182	BE2_C	brain:	n/a
14	chr5:147258132-147258182	AG04450	lung:	fetal
15	chr5:147258132-147258182	HNPCEpiC	eye:	n/a
16	chr5:147258132-147258182	CMK	blood:	n/a
17	chr5:147258132-147258182	NT2-D1	testis:	n/a
18	chr5:147258132-147258182	MCF10A-Er-Src	breast:	n/a
19	chr5:147258132-147258182	Caco-2	colon:	n/a
20	chr5:147258132-147258182	HUVEC	blood vessel:	n/a
21	chr5:147258132-147258182	HCT-116	colon:	n/a
22	chr5:147258132-147258182	NB4	blood:	n/a
23	chr5:147258132-147258182	A549	lung:	n/a
24	chr5:147258132-147258182	SK-N-SH_RA	brain:	n/a
25	chr5:147258132-147258182	HMEC	breast:	n/a
26	chr5:147258132-147258182	GM12878	blood:	n/a
27	chr5:147258132-147258182	NHBE	bronchial:	n/a
28	chr5:147258132-147258182	PFSK-1	brain:	n/a
29	chr5:147258132-147258182	Hepatocyte	liver:	n/a
30	chr5:147258132-147258182	MCF-7	breast:	n/a
31	chr5:147258132-147258182	AG10803	skin:	n/a
32	chr5:147258132-147258182	LNCaP	prostate:	n/a
33	chr5:147258132-147258182	HEK293	kidney:	embryo
34	chr5:147258132-147258182	BJ	skin:	n/a
35	chr5:147258132-147258182	IMR90	lung:	fetal
36	chr5:147258132-147258182	GM06990	blood:	n/a
37	chr5:147258132-147258182	HAEpiC	amniotic membrane:	n/a
38	chr5:147258132-147258182	RPTEC	kidney:	n/a
39	chr5:147258132-147258182	HRCEpiC	kidney:	n/a
40	chr5:147258132-147258182	SAEC	small airway:	n/a
41	chr5:147258132-147258182	PrEC	prostate:	n/a
42	chr5:147258132-147258182	HCPEpiC	choroid plexus:	n/a
43	chr5:147258132-147258182	HEEpiC	esophagus:	n/a
44	chr5:147258132-147258182	AG09309	skin:	n/a
45	chr5:147258132-147258182	PANC-1	pancreas:	n/a
46	chr5:147258132-147258182	HCF	heart:	n/a
47	chr5:147258132-147258182	HepG2	liver:	n/a
48	chr5:147258132-147258182	HPAEpiC	pulmonary alveolar:	n/a
49	chr5:147258132-147258182	SK-N-MC	brain:	n/a
50	chr5:147258132-147258182	HCM	heart:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:147255398..147258341-chr5:147264911..147267895,3	MCF-7	breast:

No data

Variant related genes	Relation type
SCGB3A2	CpG island
ENSG00000248362	Chromatin interaction
ENSG00000251320	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10036880	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10058203	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123380	0.91[CEU][hapmap];0.83[AMR][1000 genomes]
rs13355689	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13355726	0.92[CEU][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1594666	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1594667	1.00[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107353	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17107362	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17107374	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17107376	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17107378	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107379	1.00[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107380	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107381	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17107391	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2116805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2116806	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2163787	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2400646	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3910183	1.00[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3910207	1.00[CEU][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41291429	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4551056	1.00[CEU][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61012413	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6859234	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6859391	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6877288	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882292	0.81[TSI][hapmap]
rs73261378	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73261382	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7708635	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709303	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7726085	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727031	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021356	chr5:147103627-147310531	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1033907	chr5:147109014-147309076	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv537916	chr5:147109014-147309076	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3334831	chr5:147165950-147339765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv933308	chr5:147173804-147269006	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1028477	chr5:147255013-147416217	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1368408	KBTBD5	trans	parietal	SCAN
rs1368408	SPINK14	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:147234200-147262400	Weak transcription	Right Atrium	heart
2	chr5:147247600-147260200	Weak transcription	Aorta	Aorta
3	chr5:147254800-147262200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:147255200-147262000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:147255400-147258200	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr5:147255400-147258400	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:147255400-147259000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:147255400-147259800	Weak transcription	Fetal Heart	heart
9	chr5:147256000-147260000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:147256000-147262400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr5:147256200-147262400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:147256600-147262200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:147257200-147260200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:147257200-147261400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:147257400-147258400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:147257400-147260000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr5:147257800-147258200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr5:147257800-147262200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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