Variant report

Variant	rs1524773
Chromosome Location	chr1:151035171-151035172
allele	C/G
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	POLR2A	chr1:151035113-151035700	SK-N-SH	brain:	n/a	n/a
2	YY1	chr1:151035083-151035692	SK-N-SH	brain:	n/a	n/a
3	JUN	chr1:151034936-151035988	K562	blood:	n/a	chr1:151035444-151035457
4	TEAD4	chr1:151035115-151035800	K562	blood:	n/a	n/a
5	JUND	chr1:151035039-151035898	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr1:151035030-151035813	SK-N-SH	brain:	n/a	chr1:151035415-151035428
7	SIN3AK20	chr1:151035148-151035597	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr1:151035122-151035856	SK-N-SH	brain:	n/a	chr1:151035415-151035428
9	FOSL2	chr1:151035154-151035786	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:151035151-151035702	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150941235..150942777-chr1:151033520..151036344,2	K562	blood:
2	chr1:151032215..151035377-chr20:48807213..48809551,3	MCF-7	breast:
3	chr1:150976723..150987587-chr1:151024685..151036322,24	MCF-7	breast:
4	chr1:151034097..151036685-chr20:45986006..45988926,2	MCF-7	breast:
5	chr1:150996357..150999455-chr1:151032530..151036839,3	K562	blood:

Variant related genes	Relation type
CDC42SE1	TF binding region
ENSG00000143363	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000172216	Chromatin interaction
ENSG00000143418	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10749659	0.81[ASN][1000 genomes]
rs10788798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788799	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11204777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204782	1.00[JPT][hapmap]
rs11807526	1.00[JPT][hapmap]
rs12039334	0.85[EUR][1000 genomes]
rs12039542	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12087892	1.00[JPT][hapmap]
rs12117163	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12134957	0.81[ASN][1000 genomes]
rs12569193	0.85[JPT][hapmap]
rs15740	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1969442	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2067606	1.00[JPT][hapmap]
rs2140709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902810	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3738481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806386	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3806387	0.89[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4357530	0.85[JPT][hapmap]
rs4512652	0.85[JPT][hapmap]
rs4970939	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970941	0.85[JPT][hapmap]
rs4970993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970998	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970999	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971002	0.84[ASN][1000 genomes]
rs4971003	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4971006	0.84[ASN][1000 genomes]
rs4971007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971008	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs6587553	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6587557	0.85[JPT][hapmap]
rs6656450	0.85[JPT][hapmap]
rs6657593	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6668894	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6674970	0.85[JPT][hapmap]
rs6676190	1.00[JPT][hapmap]
rs6694158	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7366148	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7523731	1.00[JPT][hapmap]
rs7532312	1.00[CHB][hapmap]
rs7540258	1.00[CHB][hapmap]
rs7550434	1.00[CHB][hapmap]
rs7554936	1.00[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1524773	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs1524773	BNIPL	cis	Thyroid	GTEx
rs1524773	BNIPL	cis	lung	GTEx
rs1524773	CDC42SE1	cis	multi-tissue	Pritchard
rs1524773	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151030200-151035600	Active TSS	HSMMtube	muscle
2	chr1:151030600-151035200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:151030800-151035200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:151030800-151035400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:151030800-151035800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:151031000-151035200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:151031200-151035800	Active TSS	Brain Cingulate Gyrus	brain
8	chr1:151031400-151035600	Active TSS	Brain Angular Gyrus	brain
9	chr1:151031400-151035800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:151031600-151035200	Active TSS	Fetal Brain Female	brain
11	chr1:151031600-151035600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:151031600-151035600	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr1:151031800-151035200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:151032800-151035200	Active TSS	NH-A	brain
15	chr1:151033000-151042800	Weak transcription	Gastric	stomach
16	chr1:151033200-151035200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:151033200-151042200	Weak transcription	Esophagus	oesophagus
18	chr1:151033200-151042200	Weak transcription	Pancreas	Pancrea
19	chr1:151033200-151042600	Weak transcription	Aorta	Aorta
20	chr1:151033600-151041800	Weak transcription	Primary B cells from cord blood	blood
21	chr1:151033600-151042200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:151033800-151035200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr1:151033800-151036400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:151033800-151036600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr1:151033800-151038400	Weak transcription	Primary T cells from cord blood	blood
26	chr1:151033800-151042600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr1:151033800-151042600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:151033800-151042600	Weak transcription	Right Atrium	heart
29	chr1:151034000-151035800	Enhancers	Fetal Heart	heart
30	chr1:151034000-151036600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:151034000-151036600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:151034000-151036800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:151034000-151038200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:151034000-151038400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:151034000-151041800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr1:151034000-151041800	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:151034000-151041800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:151034000-151042000	Weak transcription	Spleen	Spleen
39	chr1:151034000-151042200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:151034000-151042400	Weak transcription	Fetal Intestine Small	intestine
41	chr1:151034200-151035200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:151034200-151035200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:151034200-151035200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:151034200-151035200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:151034200-151035200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:151034200-151035200	Weak transcription	Fetal Thymus	thymus
47	chr1:151034200-151035200	Flanking Active TSS	Dnd41	blood
48	chr1:151034200-151035200	Weak transcription	Hela-S3	cervix
49	chr1:151034200-151035200	Weak transcription	NHDF-Ad	bronchial
50	chr1:151034200-151035200	Weak transcription	NHEK	skin

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