Variant report

Variant	rs42405
Chromosome Location	chr5:14312410-14312411
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14311393..14313647-chr5:14319084..14320830,2	MCF-7	breast:
2	chr5:14306569..14308267-chr5:14310168..14313110,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11743665	1.00[ASW][hapmap]
rs12659261	0.81[EUR][1000 genomes]
rs154150	0.95[CEU][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs154153	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154154	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154155	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154161	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs165083	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16903338	0.95[CEU][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs247134	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247139	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247140	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs247141	0.90[CHB][hapmap];0.85[ASN][1000 genomes]
rs247142	0.90[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs247143	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs247144	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs256423	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs30603	0.82[EUR][1000 genomes]
rs30604	0.82[EUR][1000 genomes]
rs30605	0.82[EUR][1000 genomes]
rs30618	0.94[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs30621	0.84[MEX][hapmap]
rs30622	0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs30623	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs30624	0.81[JPT][hapmap]
rs30625	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs30632	0.82[ASN][1000 genomes]
rs30633	0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs30634	0.95[ASN][1000 genomes]
rs30635	0.81[ASN][1000 genomes]
rs30783	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs30784	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs30792	0.89[TSI][hapmap]
rs39857	0.90[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40275	0.83[ASN][1000 genomes]
rs42204	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs42259	0.80[CEU][hapmap];0.89[TSI][hapmap]
rs42551	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72744279	0.81[EUR][1000 genomes]
rs7380307	0.94[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7700787	0.90[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][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	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs42405	LOC285696	cis	parietal	SCAN
rs42405	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14270400-14313600	Weak transcription	Small Intestine	intestine
2	chr5:14278000-14341200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr5:14283000-14319400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:14286200-14320400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:14286400-14321000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr5:14286600-14314400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:14287000-14315000	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr5:14288000-14324000	Strong transcription	Primary B cells from peripheral blood	blood
9	chr5:14290800-14321200	Strong transcription	Primary B cells from cord blood	blood
10	chr5:14291400-14316600	Weak transcription	Thymus	Thymus
11	chr5:14295600-14313400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr5:14297800-14316600	Weak transcription	Brain Substantia Nigra	brain
13	chr5:14298000-14316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:14298000-14316600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr5:14299000-14314400	Strong transcription	Adipose Nuclei	Adipose
16	chr5:14299200-14315400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:14300000-14313200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:14300000-14316800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:14301200-14314000	Strong transcription	HepG2	liver
20	chr5:14302000-14313200	Weak transcription	Psoas Muscle	Psoas
21	chr5:14303600-14314400	Strong transcription	GM12878-XiMat	blood
22	chr5:14303800-14314400	Strong transcription	Liver	Liver
23	chr5:14303800-14323600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:14304000-14323800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr5:14304200-14313200	Strong transcription	Fetal Muscle Leg	muscle
26	chr5:14304200-14319400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:14304200-14321800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:14305000-14315000	Strong transcription	HMEC	breast
29	chr5:14305400-14326800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr5:14305600-14313000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:14305600-14313400	Strong transcription	NHLF	lung
32	chr5:14305600-14316400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr5:14305600-14316600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr5:14305600-14316600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr5:14305600-14317600	Strong transcription	HUVEC	blood vessel
36	chr5:14305600-14321200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:14305800-14312600	Strong transcription	HSMMtube	muscle
38	chr5:14306600-14315200	Strong transcription	A549	lung
39	chr5:14306800-14314200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:14306800-14316400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:14307000-14313400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:14307000-14314200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:14307000-14316400	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:14307200-14313600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr5:14307600-14313000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:14307600-14313800	Weak transcription	Aorta	Aorta
47	chr5:14307600-14316600	Weak transcription	Brain Angular Gyrus	brain
48	chr5:14307600-14316800	Weak transcription	Primary T cells from cord blood	blood
49	chr5:14307600-14321400	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:14307600-14321400	Strong transcription	NH-A	brain

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