Variant report

Variant	rs17394028
Chromosome Location	chr1:79117713-79117714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11162526	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11162527	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066013	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17394244	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1780746	1.00[ASN][1000 genomes]
rs55802282	0.85[AMR][1000 genomes]
rs60222720	0.97[EUR][1000 genomes]
rs72673963	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74092102	0.85[AMR][1000 genomes]
rs7526675	0.83[AMR][1000 genomes]
rs7536070	0.83[AMR][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	nsv871835	chr1:78528803-79501129	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv830315	chr1:79008443-79200591	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv871140	chr1:79095581-79155134	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17394028	MSH4	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:79115000-79118200	Active TSS	Stomach Smooth Muscle	stomach
2	chr1:79115000-79118600	Active TSS	Right Atrium	heart
3	chr1:79115200-79118000	Active TSS	NHDF-Ad	bronchial
4	chr1:79115200-79119400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:79115400-79117800	Active TSS	Brain Cingulate Gyrus	brain
6	chr1:79115400-79117800	Active TSS	Fetal Muscle Leg	muscle
7	chr1:79115400-79117800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr1:79115400-79118000	Active TSS	Lung	lung
9	chr1:79115400-79118200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:79115400-79118200	Active TSS	Left Ventricle	heart
11	chr1:79115400-79118200	Active TSS	Right Ventricle	heart
12	chr1:79115400-79118400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:79115400-79118400	Active TSS	Ovary	ovary
14	chr1:79115400-79118400	Active TSS	Rectal Smooth Muscle	rectum
15	chr1:79115400-79118400	Active TSS	Thymus	Thymus
16	chr1:79115400-79118600	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:79115400-79119000	Active TSS	Fetal Brain Female	brain
18	chr1:79115600-79118000	Weak transcription	Small Intestine	intestine
19	chr1:79115600-79118400	Active TSS	Psoas Muscle	Psoas
20	chr1:79115800-79118400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:79115800-79118600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:79116000-79124800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:79116000-79128600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:79116200-79118200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr1:79116200-79120800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:79116200-79124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr1:79116400-79127200	Weak transcription	Fetal Intestine Large	intestine
28	chr1:79116400-79129000	Weak transcription	Placenta	Placenta
29	chr1:79116400-79130000	Weak transcription	Stomach Mucosa	stomach
30	chr1:79116600-79117800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr1:79116600-79118400	Active TSS	Duodenum Mucosa	Duodenum
32	chr1:79116600-79118400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:79116800-79118200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:79116800-79118200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:79116800-79118600	Weak transcription	Fetal Kidney	kidney
36	chr1:79117000-79118400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:79117000-79124400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:79117000-79132800	Weak transcription	Fetal Brain Male	brain
39	chr1:79117200-79118200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:79117200-79118400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:79117200-79118400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:79117200-79118400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:79117200-79118600	Flanking Active TSS	Dnd41	blood
44	chr1:79117200-79119400	Active TSS	Brain Germinal Matrix	brain
45	chr1:79117200-79120600	Weak transcription	Fetal Stomach	stomach
46	chr1:79117400-79117800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:79117400-79117800	Enhancers	Primary B cells from peripheral blood	blood
48	chr1:79117400-79117800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:79117400-79118000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr1:79117400-79118200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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