Variant report

Variant	rs232774
Chromosome Location	chr1:59085443-59085444
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:59038340..59044469-chr1:59083826..59091142,23	MCF-7	breast:
2	chr1:59058111..59061332-chr1:59083852..59086894,4	MCF-7	breast:
3	chr1:59083668..59085660-chr1:59115397..59118343,2	MCF-7	breast:
4	chr1:59076652..59078644-chr1:59083527..59085617,2	K562	blood:
5	chr1:59010739..59012349-chr1:59084294..59086117,2	MCF-7	breast:
6	chr1:59035270..59037403-chr1:59084300..59086299,2	MCF-7	breast:
7	chr1:59037398..59045393-chr1:59081504..59088877,36	MCF-7	breast:
8	chr1:59048457..59052619-chr1:59081708..59087602,8	MCF-7	breast:
9	chr1:59047843..59052771-chr1:59082760..59087529,8	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184292	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1961788	0.83[EUR][1000 genomes]
rs232773	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs232803	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs232807	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs232810	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs232811	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs232812	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs232912	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003930	chr1:58930444-59157038	Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs232774	MYSM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:59082400-59087200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr1:59082600-59085800	Enhancers	HMEC	breast
3	chr1:59082600-59087600	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:59082800-59087600	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:59083000-59086400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:59083200-59086000	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:59083200-59087000	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:59083200-59088000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:59083600-59085600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:59083600-59085600	Enhancers	Colon Smooth Muscle	Colon
11	chr1:59083600-59087600	Enhancers	Stomach Mucosa	stomach
12	chr1:59083800-59085600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:59084000-59085600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:59084000-59085600	Enhancers	Psoas Muscle	Psoas
15	chr1:59084000-59085800	Enhancers	Left Ventricle	heart
16	chr1:59084000-59086000	Enhancers	Adipose Nuclei	Adipose
17	chr1:59084000-59086200	Enhancers	Primary T cells from cord blood	blood
18	chr1:59084000-59087000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:59084000-59087600	Enhancers	Lung	lung
20	chr1:59084200-59085600	Enhancers	Esophagus	oesophagus
21	chr1:59084200-59085600	Enhancers	Right Atrium	heart
22	chr1:59084200-59085600	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:59084200-59085800	Enhancers	Fetal Muscle Leg	muscle
24	chr1:59084200-59085800	Enhancers	Stomach Smooth Muscle	stomach
25	chr1:59084200-59085800	Enhancers	Spleen	Spleen
26	chr1:59084200-59086000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:59084200-59086000	Enhancers	Fetal Lung	lung
28	chr1:59084200-59086400	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr1:59084200-59086800	Enhancers	Pancreas	Pancrea
30	chr1:59084200-59087000	Enhancers	Placenta	Placenta
31	chr1:59084400-59085600	Enhancers	Brain Hippocampus Middle	brain
32	chr1:59084400-59086400	Enhancers	Fetal Thymus	thymus
33	chr1:59084600-59086400	Enhancers	HUVEC	blood vessel
34	chr1:59084800-59085600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:59084800-59085600	Enhancers	Gastric	stomach
36	chr1:59084800-59085600	Enhancers	GM12878-XiMat	blood
37	chr1:59084800-59085800	Enhancers	Thymus	Thymus
38	chr1:59084800-59086000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:59084800-59086000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr1:59084800-59086000	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr1:59084800-59086200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr1:59084800-59086400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr1:59084800-59086400	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:59085000-59086000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr1:59085000-59086000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:59085000-59086000	Enhancers	Fetal Intestine Large	intestine
47	chr1:59085000-59086200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:59085000-59086200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:59085000-59086200	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr1:59085000-59086400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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