Variant report

Variant	rs10749659
Chromosome Location	chr1:151033979-151033980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:151033762-151034410	SH-SY5Y	brain:	n/a	chr1:151033896-151033917
2	MAFK	chr1:151033591-151034136	H1-hESC	embryonic stem cell:	n/a	chr1:151033804-151033814
3	REST	chr1:151031025-151034997	H1-neurons	neurons:	n/a	chr1:151031403-151031416 chr1:151032692-151032702 chr1:151032963-151032976
4	CHD1	chr1:151029888-151034886	IMR90	lung:	n/a	n/a
5	MYC	chr1:151033709-151033981	HUVEC	blood vessel:	n/a	n/a
6	CUX1	chr1:151033756-151034098	K562	blood:	n/a	n/a
7	GATA2	chr1:151033559-151034096	SH-SY5Y	brain:	n/a	chr1:151033896-151033917
8	POLR2A	chr1:151033540-151034083	U87	brain:	n/a	n/a
9	MXI1	chr1:151029883-151034838	SK-N-SH	brain:	n/a	n/a
10	MAX	chr1:151031515-151034028	A549	lung:	n/a	chr1:151033042-151033052 chr1:151032815-151032825
11	POLR2A	chr1:151033443-151034014	SK-N-SH	brain:	n/a	n/a
12	EP300	chr1:151029972-151034687	SK-N-SH	brain:	n/a	chr1:151031911-151031920 chr1:151031778-151031794 chr1:151031908-151031924 chr1:151030872-151030881 chr1:151030649-151030663 chr1:151033804-151033811 chr1:151031736-151031750 chr1:151030871-151030885 chr1:151030308-151030322
13	POLR2A	chr1:151033434-151034035	HUVEC	blood vessel:	n/a	n/a
14	CTCF	chr1:151031501-151034126	SK-N-SH	brain:	n/a	chr1:151032811-151032824

No.	Distal block	Cell Line	Cell type
1	chr1:151005028..151012583-chr1:151026392..151034442,13	K562	blood:
2	chr1:151032665..151034303-chr1:151119415..151121131,2	MCF-7	breast:
3	chr1:150946136..150947648-chr1:151031480..151034167,2	MCF-7	breast:
4	chr1:151032358..151034155-chr1:151161962..151163858,2	MCF-7	breast:
5	chr1:151032560..151034898-chr1:151112557..151115397,2	MCF-7	breast:
6	chr1:151032375..151034566-chr1:151127124..151130341,3	K562	blood:
7	chr1:150550257..150553118-chr1:151032954..151034496,2	K562	blood:
8	chr1:150941235..150942777-chr1:151033520..151036344,2	K562	blood:
9	chr1:150967045..150969733-chr1:151032331..151034733,2	K562	blood:
10	chr1:151032215..151035377-chr20:48807213..48809551,3	MCF-7	breast:
11	chr1:150945380..150948952-chr1:151032100..151034454,3	K562	blood:
12	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
13	chr1:150996357..150999455-chr1:151032530..151036839,3	K562	blood:

Variant related genes	Relation type
CDC42SE1	TF binding region
ENSG00000143409	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000163141	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000172216	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10788800	0.87[ASN][1000 genomes]
rs11204771	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11204772	0.86[ASN][1000 genomes]
rs11204779	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12049116	0.81[EUR][1000 genomes]
rs12093562	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12134957	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1524773	0.81[ASN][1000 genomes]
rs15740	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2140709	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3738481	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806386	0.82[EUR][1000 genomes]
rs3806387	0.82[EUR][1000 genomes]
rs4357530	0.87[ASN][1000 genomes]
rs4360524	0.84[ASN][1000 genomes]
rs4970936	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970940	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4970941	0.90[ASN][1000 genomes]
rs4970993	0.81[ASN][1000 genomes]
rs61819219	0.87[ASN][1000 genomes]
rs6587552	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6656450	0.87[ASN][1000 genomes]
rs6676190	0.87[ASN][1000 genomes]
rs6697617	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6704195	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7414477	0.85[ASN][1000 genomes]
rs7522608	0.95[ASN][1000 genomes]
rs7536234	0.86[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
rs10749659	BNIPL	cis	lung	GTEx
rs10749659	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs10749659	BNIPL	cis	Thyroid	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151030200-151035600	Active TSS	HSMMtube	muscle
2	chr1:151030400-151034200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151030400-151034400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:151030600-151034800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151030600-151035200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:151030800-151034000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:151030800-151034000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:151030800-151034200	Active TSS	H9 Cell Line	embryonic stem cell
9	chr1:151030800-151034200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:151030800-151034400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:151030800-151034400	Active TSS	NHLF	lung
12	chr1:151030800-151034600	Active TSS	Thymus	Thymus
13	chr1:151030800-151034800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:151030800-151035200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:151030800-151035400	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr1:151030800-151035800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:151031000-151034000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:151031000-151034000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:151031000-151034400	Active TSS	HSMM	muscle
20	chr1:151031000-151034600	Active TSS	Brain Anterior Caudate	brain
21	chr1:151031000-151034600	Active TSS	A549	lung
22	chr1:151031000-151035200	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr1:151031200-151034000	Active TSS	Fetal Intestine Small	intestine
24	chr1:151031200-151034200	Active TSS	H1 Cell Line	embryonic stem cell
25	chr1:151031200-151034600	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr1:151031200-151034800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:151031200-151035800	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:151031400-151034200	Active TSS	Fetal Intestine Large	intestine
29	chr1:151031400-151034200	Active TSS	Fetal Muscle Trunk	muscle
30	chr1:151031400-151034800	Active TSS	Fetal Brain Male	brain
31	chr1:151031400-151035600	Active TSS	Brain Angular Gyrus	brain
32	chr1:151031400-151035800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:151031600-151034200	Active TSS	Dnd41	blood
34	chr1:151031600-151035200	Active TSS	Fetal Brain Female	brain
35	chr1:151031600-151035600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:151031600-151035600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:151031800-151034600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:151031800-151035200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:151032200-151034000	Flanking Active TSS	NHEK	skin
40	chr1:151032200-151034200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr1:151032200-151034600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:151032800-151034000	Flanking Active TSS	HMEC	breast
43	chr1:151032800-151034200	Enhancers	Hela-S3	cervix
44	chr1:151032800-151034800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:151032800-151035200	Active TSS	NH-A	brain
46	chr1:151033000-151042800	Weak transcription	Gastric	stomach
47	chr1:151033200-151034000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:151033200-151034000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr1:151033200-151034000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr1:151033200-151034000	Active TSS	Skeletal Muscle Female	skeletal muscle

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