Variant report

Variant	rs10059138
Chromosome Location	chr5:95170719-95170720
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	chr5:94981172..94985318-chr5:95169805..95176246,5	MCF-7	breast:
2	chr5:95157133..95161008-chr5:95170364..95173601,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GLRX-2	chr5:95170611-95170750	NONHSAT102864

Variant related genes	Relation type
ENSG00000175449	Chromatin interaction
ENSG00000173221	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10040697	0.81[CEU][hapmap]
rs10059130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10059245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067881	1.00[ASN][1000 genomes]
rs10074815	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10515230	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57148774	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6556884	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556885	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556886	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6556891	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67807434	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68044534	0.94[ASN][1000 genomes]
rs68095140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72785409	1.00[ASN][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	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015180	chr5:95134357-95286446	Strong transcription Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv882389	chr5:95144952-95173887	Strong transcription Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10059138	AC008592.3	cis	Whole Blood	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95161600-95171400	Weak transcription	Small Intestine	intestine
2	chr5:95164200-95171400	Weak transcription	Spleen	Spleen
3	chr5:95169800-95171200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:95169800-95171400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:95169800-95171400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr5:95169800-95171400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:95169800-95171400	Active TSS	Right Ventricle	heart
8	chr5:95169800-95171600	Active TSS	Rectal Smooth Muscle	rectum
9	chr5:95169800-95171600	Active TSS	Stomach Smooth Muscle	stomach
10	chr5:95169800-95171800	Active TSS	Brain Cingulate Gyrus	brain
11	chr5:95170000-95170800	Active TSS	Primary hematopoietic stem cells	blood
12	chr5:95170000-95170800	Active TSS	Thymus	Thymus
13	chr5:95170000-95171000	Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr5:95170000-95171000	Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr5:95170000-95171000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:95170000-95171000	Active TSS	Fetal Kidney	kidney
17	chr5:95170000-95171200	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr5:95170000-95171200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:95170000-95171200	Active TSS	Brain Anterior Caudate	brain
20	chr5:95170000-95171200	Active TSS	Brain Hippocampus Middle	brain
21	chr5:95170000-95171200	Active TSS	Duodenum Mucosa	Duodenum
22	chr5:95170000-95171200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr5:95170000-95171200	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:95170000-95171200	Active TSS	A549	lung
25	chr5:95170000-95171200	Active TSS	Hela-S3	cervix
26	chr5:95170000-95171400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr5:95170000-95171400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr5:95170000-95171400	Active TSS	Right Atrium	heart
29	chr5:95170000-95171400	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr5:95170000-95171400	Active TSS	GM12878-XiMat	blood
31	chr5:95170000-95172200	Active TSS	Psoas Muscle	Psoas
32	chr5:95170200-95170800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr5:95170200-95170800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:95170200-95170800	Active TSS	Primary T cells from cord blood	blood
35	chr5:95170200-95170800	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr5:95170200-95170800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr5:95170200-95170800	Active TSS	HSMMtube	muscle
38	chr5:95170200-95170800	Active TSS	NH-A	brain
39	chr5:95170200-95171000	Active TSS	H1 Cell Line	embryonic stem cell
40	chr5:95170200-95171000	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr5:95170200-95171000	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr5:95170200-95171000	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr5:95170200-95171000	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr5:95170200-95171000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr5:95170200-95171000	Active TSS	Adipose Nuclei	Adipose
46	chr5:95170200-95171000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr5:95170200-95171000	Active TSS	Fetal Brain Female	brain
48	chr5:95170200-95171000	Active TSS	Fetal Lung	lung
49	chr5:95170200-95171000	Active TSS	Fetal Muscle Leg	muscle
50	chr5:95170200-95171000	Active TSS	Fetal Stomach	stomach

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