Variant report

Variant	rs1704407
Chromosome Location	chr15:42250551-42250552
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:42248315..42251677-chr15:42258247..42261480,4	MCF-7	breast:
2	chr15:42248239..42251142-chr15:42253260..42256152,2	K562	blood:
3	chr15:42246217..42248184-chr15:42249664..42252463,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11549015	0.89[CEU][hapmap];1.00[LWK][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12910173	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1704405	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap]
rs35796146	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36018108	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3816533	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
4	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
5	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
8	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1704407	DUSP21	trans	parietal	SCAN
rs1704407	BUB1B	cis	parietal	SCAN
rs1704407	LCMT2	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42230400-42262200	Weak transcription	Thymus	Thymus
2	chr15:42240400-42251800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:42240400-42252600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr15:42241200-42259200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:42242000-42250800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:42242600-42251200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr15:42243000-42252000	Weak transcription	A549	lung
8	chr15:42244200-42253200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:42244200-42259400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:42244400-42260600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr15:42245800-42253000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:42246000-42253200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:42246000-42253200	Weak transcription	HMEC	breast
14	chr15:42246000-42253400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:42246200-42253400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:42246200-42253400	Weak transcription	Duodenum Mucosa	Duodenum
17	chr15:42246200-42254600	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:42246200-42261800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:42246200-42261800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:42246200-42262000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:42246200-42262000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr15:42246400-42258400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:42246400-42259800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:42246400-42262200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:42246600-42253200	Weak transcription	Hela-S3	cervix
26	chr15:42246600-42258000	Weak transcription	Fetal Stomach	stomach
27	chr15:42246600-42261800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:42247400-42250600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr15:42247400-42250600	Enhancers	Right Atrium	heart
30	chr15:42247400-42250600	Enhancers	Right Ventricle	heart
31	chr15:42247400-42250600	Enhancers	Spleen	Spleen
32	chr15:42247400-42250800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr15:42247400-42250800	Enhancers	Fetal Muscle Leg	muscle
34	chr15:42247600-42251000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:42247800-42258200	Weak transcription	NHLF	lung
36	chr15:42248000-42250600	Enhancers	Fetal Intestine Large	intestine
37	chr15:42248000-42250600	Genic enhancers	HSMM	muscle
38	chr15:42248000-42250800	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:42248000-42250800	Strong transcription	NHEK	skin
40	chr15:42248400-42251400	Enhancers	Liver	Liver
41	chr15:42248400-42253200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:42248400-42257600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:42248600-42250600	Enhancers	Adipose Nuclei	Adipose
44	chr15:42248600-42251600	Enhancers	Left Ventricle	heart
45	chr15:42248600-42253200	Weak transcription	HepG2	liver
46	chr15:42248600-42253200	Weak transcription	HSMMtube	muscle
47	chr15:42248600-42258200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:42248600-42258200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:42248600-42258400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:42248600-42263400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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