Variant report

Variant	rs9803935
Chromosome Location	chr1:150552622-150552623
allele	G/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	POLR2A	chr1:150546850-150552818	GM12878	blood:	n/a	n/a
2	MAX	chr1:150551063-150552871	H1-hESC	embryonic stem cell:	n/a	chr1:150552667-150552677 chr1:150552667-150552677 chr1:150552666-150552677 chr1:150552668-150552675 chr1:150552667-150552676
3	POLR2A	chr1:150551528-150552844	SK-N-SH	brain:	n/a	n/a
4	MYC	chr1:150551800-150552814	H1-hESC	embryonic stem cell:	n/a	chr1:150552667-150552677 chr1:150552667-150552677 chr1:150552666-150552677 chr1:150552668-150552675 chr1:150552667-150552676
5	ARID3A	chr1:150551901-150552649	HepG2	liver:	n/a	n/a
6	CEBPB	chr1:150550798-150552753	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:150552245-150552692	GM12892	blood:	n/a	n/a
8	RELA	chr1:150551842-150552691	GM12892	blood:	n/a	n/a
9	ELF1	chr1:150551591-150552716	HCT-116	colon:	n/a	chr1:150552014-150552023 chr1:150552070-150552079 chr1:150552067-150552080 chr1:150552017-150552026
10	SRF	chr1:150550634-150552910	MCF-7	breast:	n/a	chr1:150551994-150552009 chr1:150552167-150552185 chr1:150552169-150552187 chr1:150552172-150552189 chr1:150552170-150552185
11	POLR2A	chr1:150550237-150552750	GM19099	blood:	n/a	n/a
12	TBL1XR1	chr1:150551571-150552735	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:150546864-150552806	GM18505	blood:	n/a	n/a
14	SIN3AK20	chr1:150550672-150552836	HCT-116	colon:	n/a	n/a
15	ZKSCAN1	chr1:150550788-150552743	Hela-S3	cervix:	n/a	n/a
16	CREB1	chr1:150550768-150552671	H1-hESC	embryonic stem cell:	n/a	n/a
17	RELA	chr1:150550817-150552622	GM18951	blood:	n/a	n/a
18	POLR2A	chr1:150550168-150552761	HUVEC	blood vessel:	n/a	n/a
19	REST	chr1:150549530-150553038	H1-neurons	neurons:	n/a	chr1:150552093-150552101
20	FOSL2	chr1:150550462-150552671	A549	lung:	n/a	chr1:150551163-150551174
21	TEAD4	chr1:150549117-150552737	K562	blood:	n/a	n/a
22	ELK1	chr1:150550742-150552648	Hela-S3	cervix:	n/a	n/a
23	EP300	chr1:150551822-150552698	K562	blood:	n/a	chr1:150552342-150552358 chr1:150552015-150552024 chr1:150552069-150552083
24	ELF1	chr1:150551580-150552726	HCT-116	colon:	n/a	chr1:150552014-150552023 chr1:150552070-150552079 chr1:150552067-150552080 chr1:150552017-150552026
25	RELA	chr1:150551842-150552634	GM19099	blood:	n/a	n/a
26	MAX	chr1:150552446-150552708	H1-hESC	embryonic stem cell:	n/a	chr1:150552667-150552677 chr1:150552667-150552677 chr1:150552666-150552677 chr1:150552668-150552675 chr1:150552667-150552676
27	POLR2A	chr1:150550660-150553289	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:150550505-150553020	K562	blood:	n/a	n/a
29	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
30	TAF1	chr1:150550852-150552627	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr1:150549143-150552715	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr1:150551016-150552743	K562	blood:	n/a	n/a
33	PML	chr1:150550856-150552762	MCF-7	breast:	n/a	n/a
34	POLR2A	chr1:150550177-150552629	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:150546598-150553153	U87	brain:	n/a	n/a
36	POLR2A	chr1:150552271-150552658	HL-60	blood:	n/a	n/a
37	POLR2A	chr1:150546807-150552855	SK-N-SH	brain:	n/a	n/a
38	MTA3	chr1:150552264-150552848	GM12878	blood:	n/a	n/a
39	PML	chr1:150551420-150552666	K562	blood:	n/a	n/a
40	POLR2A	chr1:150550241-150552766	GM12878	blood:	n/a	n/a
41	MYBL2	chr1:150551792-150552683	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:150527732-150552686	MCF10A-Er-Src	breast:	n/a	n/a
43	PML	chr1:150550867-150552649	MCF-7	breast:	n/a	n/a
44	SP1	chr1:150551508-150552640	H1-hESC	embryonic stem cell:	n/a	chr1:150552185-150552192
45	POLR2A	chr1:150550143-150552808	H1-neurons	neurons:	n/a	n/a
46	CHD1	chr1:150546653-150553181	IMR90	lung:	n/a	n/a
47	POLR2A	chr1:150530622-150553130	IMR90	lung:	n/a	n/a
48	POLR2A	chr1:150550729-150552756	ProgFib	skin:	n/a	n/a
49	GABPA	chr1:150550809-150552736	MCF-7	breast:	n/a	chr1:150552070-150552077
50	POLR2A	chr1:150552275-150552658	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:150549047..150553046-chr1:150599453..150603954,9	MCF-7	breast:
2	chr1:150547986..150553838-chr1:150598744..150606232,19	K562	blood:
3	chr1:150538995..150557554-chr1:150581886..150604495,126	K562	blood:
4	chr1:150548752..150555486-chr1:150599368..150605834,15	MCF-7	breast:
5	chr1:150336951..150339274-chr1:150551327..150552882,2	K562	blood:
6	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
7	chr1:150551507..150553628-chr1:150668472..150670953,2	K562	blood:
8	chr1:150550567..150552845-chr1:151042071..151045056,2	MCF-7	breast:
9	chr1:150550164..150555275-chr1:150782862..150788394,7	MCF-7	breast:
10	chr1:150550706..150553008-chr1:150788888..150791389,2	K562	blood:
11	chr1:150550605..150553329-chr1:151136705..151138908,2	K562	blood:
12	chr1:150458615..150462130-chr1:150550221..150553114,4	K562	blood:
13	chr1:150551078..150552936-chr1:150667990..150671349,4	K562	blood:
14	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
15	chr1:150551863..150552672-chr2:43453330..43454322,2	MCF-7	breast:
16	chr1:150521298..150527553-chr1:150548198..150553572,10	MCF-7	breast:
17	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
18	chr1:150552057..150552895-chr7:139025854..139026496,2	Hela-S3	cervix:
19	chr1:150551989..150552685-chr17:15554385..15554952,2	MCF-7	breast:
20	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:
21	chr1:150551961..150552659-chr6:35888288..35889046,2	HCT-116	colon:
22	chr1:150551378..150553300-chr1:150944488..150946159,2	MCF-7	breast:
23	chr1:150549378..150552816-chr1:151028901..151032004,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADAMTSL4-5	chr1:150552352-150552695	NONHSAT006316

Variant related genes	Relation type
MCL1	TF binding region
ENSG00000213190	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000266261	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000096063	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000264553	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000143437	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1053732	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10888384	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10888385	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204668	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204669	0.93[ASN][1000 genomes]
rs11204675	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204677	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204678	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204679	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204680	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204684	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11585169	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12116492	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12125672	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126271	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12139563	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12406712	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12746899	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1971378	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2048558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738485	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754209	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970918	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970923	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971041	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55862611	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61820165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669122	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6697620	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs878471	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs932054	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv535155	chr1:150535349-150582395	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
3	nsv535156	chr1:150540117-150575941	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs9803935	HORMAD1	cis	normal skin	skin_eQTL
rs9803935	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs9803935	HORMAD1	cis	Esophagus Mucosa	GTEx
rs9803935	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs9803935	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs9803935	ARNT	cis	Thyroid	GTEx
rs9803935	ARNT	cis	normal skin	skin_eQTL
rs9803935	GOLPH3L	cis	Nerve Tibial	GTEx
rs9803935	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs9803935	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs9803935	HORMAD1	cis	uninvolved skin	skin_eQTL
rs9803935	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs9803935	HORMAD1	cis	Nerve Tibial	GTEx
rs9803935	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs9803935	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs9803935	HORMAD1	cis	lesional skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150547600-150552800	Active TSS	Ovary	ovary
2	chr1:150548200-150552800	Active TSS	Aorta	Aorta
3	chr1:150548600-150553000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:150549000-150553000	Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr1:150549200-150553000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:150549600-150552800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:150549800-150552800	Active TSS	Psoas Muscle	Psoas
8	chr1:150550000-150552800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:150550000-150552800	Active TSS	Lung	lung
10	chr1:150550000-150552800	Active TSS	Pancreas	Pancrea
11	chr1:150550000-150553000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:150550200-150552800	Active TSS	Liver	Liver
13	chr1:150550400-150552800	Active TSS	Right Ventricle	heart
14	chr1:150550800-150553000	Active TSS	GM12878-XiMat	blood
15	chr1:150551000-150553000	Active TSS	Colonic Mucosa	Colon
16	chr1:150551000-150553000	Active TSS	HSMM	muscle
17	chr1:150551200-150553000	Active TSS	Thymus	Thymus
18	chr1:150551400-150552800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr1:150551400-150552800	Active TSS	Sigmoid Colon	Sigmoid Colon
20	chr1:150551400-150553000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr1:150551400-150553200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:150551400-150553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:150551600-150552800	Active TSS	H9 Cell Line	embryonic stem cell
24	chr1:150551600-150552800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:150551600-150552800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:150551600-150552800	Active TSS	Left Ventricle	heart
27	chr1:150551800-150553000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:150552000-150552800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:150552000-150553800	Weak transcription	Gastric	stomach
30	chr1:150552200-150552800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:150552200-150552800	Active TSS	Brain Germinal Matrix	brain
32	chr1:150552200-150552800	Flanking Active TSS	Fetal Thymus	thymus
33	chr1:150552200-150552800	Active TSS	Right Atrium	heart
34	chr1:150552400-150552800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:150552400-150552800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr1:150552400-150552800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:150552400-150552800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr1:150552400-150552800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr1:150552400-150552800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:150552400-150552800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr1:150552400-150552800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr1:150552400-150552800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:150552400-150552800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr1:150552400-150552800	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr1:150552400-150552800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:150552400-150552800	Flanking Active TSS	Placenta	Placenta
47	chr1:150552400-150552800	Flanking Active TSS	A549	lung
48	chr1:150552400-150553000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
49	chr1:150552400-150553000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:150552400-150553000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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