Variant report

Variant	rs4970990
Chromosome Location	chr1:151003704-151003705
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
2	chr1:151000441..151004235-chr1:151011112..151014121,3	MCF-7	breast:
3	chr1:151001747..151004100-chr1:151008531..151011472,2	K562	blood:
4	chr1:150997048..150999489-chr1:151001423..151004398,3	MCF-7	breast:
5	chr1:150996555..150999448-chr1:151003489..151006449,2	K562	blood:
6	chr1:151002944..151005069-chr1:151149022..151151363,2	MCF-7	breast:
7	chr1:150997115..151004935-chr1:151005196..151010372,8	MCF-7	breast:
8	chr1:151002864..151005817-chr1:151007224..151009647,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction
ENSG00000163141	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10788797	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs1969442	0.96[ASN][1000 genomes]
rs2902810	0.92[ASN][1000 genomes]
rs35550545	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738476	0.86[AMR][1000 genomes]
rs3806386	0.82[ASN][1000 genomes]
rs3806387	0.82[ASN][1000 genomes]
rs6587553	0.94[ASN][1000 genomes]
rs6657593	0.96[ASN][1000 genomes]
rs6694158	0.96[ASN][1000 genomes]
rs7366148	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7532312	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7540258	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7550434	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4970990	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970990	BNIPL	cis	lung	GTEx
rs4970990	BNIPL	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150981800-151006400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:150982000-151009000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:150984200-151006400	Weak transcription	HMEC	breast
4	chr1:150986200-151006200	Weak transcription	Pancreas	Pancrea
5	chr1:150989800-151010400	Strong transcription	Fetal Stomach	stomach
6	chr1:150996000-151006600	Weak transcription	NH-A	brain
7	chr1:150996200-151008400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:150996600-151009200	Strong transcription	Fetal Intestine Large	intestine
9	chr1:150996600-151009800	Strong transcription	Fetal Intestine Small	intestine
10	chr1:150996800-151004400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr1:150997000-151007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:150997000-151008000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:150997000-151008200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:150997200-151005000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:150997200-151005000	Strong transcription	Placenta	Placenta
16	chr1:150997200-151005000	Strong transcription	Osteobl	bone
17	chr1:150997200-151005200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:150997200-151008000	Strong transcription	Dnd41	blood
19	chr1:150997400-151004400	Strong transcription	Primary T cells from cord blood	blood
20	chr1:150997400-151004400	Strong transcription	Brain Anterior Caudate	brain
21	chr1:150997400-151004600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:150997400-151004800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr1:150997400-151005000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:150997400-151005000	Strong transcription	Thymus	Thymus
25	chr1:150997400-151006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr1:150997400-151007400	Weak transcription	Stomach Mucosa	stomach
27	chr1:150997400-151008000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:150997400-151008000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:150997400-151008000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:150997400-151008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:150997400-151008400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:150997400-151009400	Strong transcription	Fetal Thymus	thymus
33	chr1:150997400-151009800	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:150997600-151004400	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr1:150997600-151004600	Strong transcription	Primary B cells from peripheral blood	blood
36	chr1:150997600-151005000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr1:150997600-151008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:150997600-151008000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:150997600-151008200	Strong transcription	Adipose Nuclei	Adipose
40	chr1:150997600-151008800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:150997600-151009400	Strong transcription	Liver	Liver
42	chr1:150997600-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:150997600-151019800	Weak transcription	HUVEC	blood vessel
44	chr1:150997800-151004400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:150997800-151004400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:150997800-151004600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:150997800-151005000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:150997800-151005000	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:150997800-151008400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:150997800-151019800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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