Variant report

Variant	rs6503545
Chromosome Location	chr17:38798073-38798074
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38797378..38799049-chr17:38859187..38861581,2	MCF-7	breast:
2	chr17:38796377..38799257-chr17:38854775..38858682,3	MCF-7	breast:
3	chr17:38798051..38800892-chr17:38851970..38854604,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167916	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11078950	0.87[EUR][1000 genomes]
rs11650910	0.87[EUR][1000 genomes]
rs11654834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11659024	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11869540	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1474454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1526601	0.90[EUR][1000 genomes]
rs16966093	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961204	0.80[EUR][1000 genomes]
rs2011870	0.87[EUR][1000 genomes]
rs2429547	0.86[EUR][1000 genomes]
rs2429548	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.88[EUR][1000 genomes]
rs2429550	0.80[EUR][1000 genomes]
rs2429551	0.96[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs2429552	0.88[CEU][hapmap]
rs2462957	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs2462960	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes]
rs2462961	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs2462965	0.80[EUR][1000 genomes]
rs2462966	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2462969	0.92[CEU][hapmap]
rs2469817	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2469820	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs2469825	0.96[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs55664118	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6503546	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67138687	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7218478	0.82[AFR][1000 genomes]
rs7224919	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs723728	0.88[CEU][hapmap]
rs723729	0.88[CEU][hapmap]
rs726849	0.89[CEU][hapmap]
rs8065040	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8066541	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8074179	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8074758	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs874889	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs887376	0.92[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs9303294	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes]
rs9630729	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9675112	0.85[CEU][hapmap]
rs9894823	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9902509	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6503545	KRT24	cis	Esophagus Mucosa	GTEx
rs6503545	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs6503545	SMARCE1	cis	multi-tissue	Pritchard
rs6503545	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38782600-38801000	Strong transcription	Primary B cells from cord blood	blood
2	chr17:38783000-38800200	Strong transcription	Duodenum Mucosa	Duodenum
3	chr17:38783000-38802400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr17:38783200-38799200	Strong transcription	Fetal Muscle Leg	muscle
5	chr17:38783200-38800600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr17:38783200-38800800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr17:38783200-38800800	Strong transcription	GM12878-XiMat	blood
8	chr17:38783200-38801400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr17:38783200-38801400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:38783200-38801400	Strong transcription	A549	lung
11	chr17:38783200-38801600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr17:38783200-38801800	Strong transcription	Fetal Thymus	thymus
13	chr17:38783200-38801800	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr17:38783400-38800400	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr17:38783400-38800600	Strong transcription	Primary T cells from cord blood	blood
16	chr17:38783400-38801400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr17:38783400-38801400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:38783400-38801400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr17:38783400-38801600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:38783400-38801600	Strong transcription	Liver	Liver
21	chr17:38783400-38802000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:38783400-38802200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr17:38783600-38800800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr17:38783600-38801600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr17:38783600-38802400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr17:38783800-38801400	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr17:38783800-38802800	Strong transcription	Placenta	Placenta
28	chr17:38784000-38799200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr17:38784000-38801600	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr17:38784200-38799200	Strong transcription	NHDF-Ad	bronchial
31	chr17:38784200-38801800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr17:38784200-38802000	Strong transcription	Hela-S3	cervix
33	chr17:38784400-38800200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:38784400-38800400	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr17:38784400-38800600	Strong transcription	HUVEC	blood vessel
36	chr17:38784400-38802000	Strong transcription	Osteobl	bone
37	chr17:38784600-38801400	Strong transcription	Primary hematopoietic stem cells	blood
38	chr17:38784600-38801800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:38784600-38802000	Strong transcription	Fetal Intestine Large	intestine
40	chr17:38785600-38801600	Strong transcription	HSMM	muscle
41	chr17:38786000-38801000	Strong transcription	Fetal Lung	lung
42	chr17:38786000-38802000	Strong transcription	K562	blood
43	chr17:38786200-38801200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr17:38787000-38802600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:38787200-38802600	Weak transcription	Psoas Muscle	Psoas
46	chr17:38788200-38799000	Strong transcription	Thymus	Thymus
47	chr17:38788400-38798600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr17:38789200-38803000	Weak transcription	Stomach Mucosa	stomach
49	chr17:38789600-38803400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr17:38790600-38802400	Weak transcription	Small Intestine	intestine

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