Variant report

Variant	rs4589116
Chromosome Location	chr1:151002510-151002511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151001376..151003015-chr1:151029342..151030894,2	K562	blood:
2	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
3	chr1:151000441..151004235-chr1:151011112..151014121,3	MCF-7	breast:
4	chr1:151001747..151004100-chr1:151008531..151011472,2	K562	blood:
5	chr1:150997048..150999489-chr1:151001423..151004398,3	MCF-7	breast:
6	chr1:150997115..151004935-chr1:151005196..151010372,8	MCF-7	breast:
7	chr1:150995615..151002939-chr1:151018225..151024612,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143363	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000143443	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10788797	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091219	0.98[ASN][1000 genomes]
rs2864700	0.84[ASN][1000 genomes]
rs2902811	0.91[ASN][1000 genomes]
rs3738476	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970989	1.00[ASN][1000 genomes]
rs4970991	1.00[ASN][1000 genomes]
rs6587552	0.89[ASN][1000 genomes]
rs6691701	1.00[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4589116	BNIPL	cis	Thyroid	GTEx
rs4589116	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

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	chr1:150982200-151002800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:150984200-151006400	Weak transcription	HMEC	breast
5	chr1:150986000-151003200	Weak transcription	Fetal Brain Male	brain
6	chr1:150986200-151006200	Weak transcription	Pancreas	Pancrea
7	chr1:150989800-151010400	Strong transcription	Fetal Stomach	stomach
8	chr1:150993000-151003200	Weak transcription	NHDF-Ad	bronchial
9	chr1:150996000-151006600	Weak transcription	NH-A	brain
10	chr1:150996200-151008400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:150996600-151009200	Strong transcription	Fetal Intestine Large	intestine
12	chr1:150996600-151009800	Strong transcription	Fetal Intestine Small	intestine
13	chr1:150996800-151004400	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr1:150997000-151007800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:150997000-151008000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:150997000-151008200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:150997200-151005000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:150997200-151005000	Strong transcription	Placenta	Placenta
19	chr1:150997200-151005000	Strong transcription	Osteobl	bone
20	chr1:150997200-151005200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:150997200-151008000	Strong transcription	Dnd41	blood
22	chr1:150997400-151004400	Strong transcription	Primary T cells from cord blood	blood
23	chr1:150997400-151004400	Strong transcription	Brain Anterior Caudate	brain
24	chr1:150997400-151004600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:150997400-151004800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:150997400-151005000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:150997400-151005000	Strong transcription	Thymus	Thymus
28	chr1:150997400-151006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr1:150997400-151007400	Weak transcription	Stomach Mucosa	stomach
30	chr1:150997400-151008000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:150997400-151008000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:150997400-151008000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:150997400-151008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:150997400-151008400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:150997400-151009400	Strong transcription	Fetal Thymus	thymus
36	chr1:150997400-151009800	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:150997600-151003200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:150997600-151003200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:150997600-151004400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:150997600-151004600	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:150997600-151005000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:150997600-151008000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:150997600-151008000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:150997600-151008200	Strong transcription	Adipose Nuclei	Adipose
45	chr1:150997600-151008800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr1:150997600-151009400	Strong transcription	Liver	Liver
47	chr1:150997600-151015400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:150997600-151019800	Weak transcription	HUVEC	blood vessel
49	chr1:150997800-151004400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:150997800-151004400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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