Variant report

Variant	rs1355642
Chromosome Location	chr1:46598903-46598904
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	MAZ	chr1:46598056-46599249	Hela-S3	cervix:	n/a	n/a
2	NRF1	chr1:46598177-46598917	H1-hESC	embryonic stem cell:	n/a	chr1:46598764-46598775
3	MAX	chr1:46598042-46599389	HepG2	liver:	n/a	n/a
4	GABPA	chr1:46598031-46599346	K562	blood:	n/a	n/a
5	CBX3	chr1:46597846-46599310	K562	blood:	n/a	n/a
6	POLR2A	chr1:46597328-46599465	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr1:46597226-46599439	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:46597963-46599381	Hela-S3	cervix:	n/a	n/a
9	CCNT2	chr1:46597988-46599182	K562	blood:	n/a	n/a
10	CREB1	chr1:46598032-46599318	HepG2	liver:	n/a	n/a
11	SP1	chr1:46597994-46599276	A549	lung:	n/a	chr1:46598783-46598804 chr1:46598351-46598360 chr1:46598679-46598700 chr1:46598351-46598364 chr1:46598350-46598359 chr1:46598350-46598359
12	POLR2A	chr1:46598553-46599147	H1-hESC	embryonic stem cell:	n/a	n/a
13	EP300	chr1:46598155-46599142	T-47D	breast:	n/a	chr1:46598803-46598812 chr1:46598799-46598815 chr1:46598801-46598810
14	POLR2A	chr1:46597267-46599352	SK-N-SH	brain:	n/a	n/a
15	NANOG	chr1:46598499-46598954	H1-hESC	embryonic stem cell:	n/a	chr1:46598847-46598861
16	POLR2A	chr1:46598162-46598980	HL-60	blood:	n/a	n/a
17	MAX	chr1:46598097-46599273	NB4	blood:	n/a	n/a
18	POLR2A	chr1:46597625-46599494	ECC-1	luminal epithelium:	n/a	n/a
19	UBTF	chr1:46597325-46599320	K562	blood:	n/a	n/a
20	EP300	chr1:46598123-46599169	MCF-7	breast:	n/a	chr1:46598803-46598812 chr1:46598799-46598815 chr1:46598801-46598810
21	POLR2A	chr1:46597697-46599402	K562	blood:	n/a	n/a
22	MAX	chr1:46598021-46599408	MCF-7	breast:	n/a	n/a
23	PBX3	chr1:46597967-46599360	SK-N-SH	brain:	n/a	chr1:46598785-46598794
24	POLR2A	chr1:46597981-46599466	GM12892	blood:	n/a	n/a
25	TBP	chr1:46596893-46599072	Hela-S3	cervix:	n/a	n/a
26	RELA	chr1:46597848-46599324	GM19099	blood:	n/a	n/a
27	TBP	chr1:46598089-46598926	GM12878	blood:	n/a	n/a
28	EP300	chr1:46598410-46598949	HepG2	liver:	n/a	chr1:46598803-46598812 chr1:46598799-46598815 chr1:46598801-46598810
29	POLR2A	chr1:46597980-46599351	GM12878	blood:	n/a	n/a
30	MYC	chr1:46598056-46599260	K562	blood:	n/a	n/a
31	POLR2A	chr1:46598540-46599262	K562	blood:	n/a	n/a
32	POLR2A	chr1:46597936-46599449	HUVEC	blood vessel:	n/a	n/a
33	MAX	chr1:46598405-46599249	H1-hESC	embryonic stem cell:	n/a	n/a
34	FOXM1	chr1:46598009-46599321	ECC-1	luminal epithelium:	n/a	n/a
35	HEY1	chr1:46598850-46599323	K562	blood:	n/a	n/a
36	MYBL2	chr1:46598114-46599129	HepG2	liver:	n/a	n/a
37	GTF2F1	chr1:46597929-46599327	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr1:46597834-46599491	GM12892	blood:	n/a	n/a
39	SIN3A	chr1:46597078-46599412	H1-hESC	embryonic stem cell:	n/a	chr1:46598597-46598606
40	SP1	chr1:46598069-46599371	HCT-116	colon:	n/a	chr1:46598783-46598804 chr1:46598351-46598360 chr1:46598679-46598700 chr1:46598351-46598364 chr1:46598350-46598359 chr1:46598350-46598359
41	POLR2A	chr1:46596953-46600001	GM12891	blood:	n/a	n/a
42	EP300	chr1:46597416-46598999	K562	blood:	n/a	chr1:46598803-46598812 chr1:46597493-46597507 chr1:46598799-46598815 chr1:46598014-46598028 chr1:46598801-46598810
43	CBX3	chr1:46597893-46599305	HCT-116	colon:	n/a	n/a
44	POLR2A	chr1:46598051-46599256	K562	blood:	n/a	n/a
45	BRCA1	chr1:46597463-46599014	Hela-S3	cervix:	n/a	n/a
46	MYC	chr1:46597782-46599077	MCF10A-Er-Src	breast:	n/a	n/a
47	EP300	chr1:46598117-46598989	HepG2	liver:	n/a	chr1:46598803-46598812 chr1:46598799-46598815 chr1:46598801-46598810
48	ATF2	chr1:46598425-46599135	H1-hESC	embryonic stem cell:	n/a	n/a
49	NFIC	chr1:46597778-46599322	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:46598579-46599293	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46596666..46599509-chr1:46766938..46769166,2	K562	blood:
2	chr1:46598178..46600574-chr1:46641246..46642770,2	K562	blood:
3	chr1:46597687..46601092-chr1:46685533..46687921,3	MCF-7	breast:
4	chr1:46152742..46154497-chr1:46598104..46600234,2	K562	blood:
5	chr1:46598353..46599286-chr6:31628150..31628675,2	NB4	blood:
6	chr1:46596732..46600061-chr1:46639198..46641036,3	K562	blood:
7	chr1:46596539..46599415-chr1:46667478..46670320,3	K562	blood:
8	chr1:46596990..46600235-chr1:46653510..46656266,3	K562	blood:
9	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
10	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
11	chr1:46498806..46500907-chr1:46597285..46600123,2	MCF-7	breast:
12	chr1:46598229..46599012-chr6:86388363..86388922,2	Hela-S3	cervix:
13	chr1:46595820..46599539-chr1:46766607..46769915,4	K562	blood:
14	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
15	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
16	chr1:46598477..46601244-chr1:46712967..46714555,2	K562	blood:
17	chr1:46597413..46599611-chr12:6976229..6978931,2	K562	blood:
18	chr1:46596689..46599415-chr1:46667615..46670320,3	K562	blood:
19	chr1:46498325..46500159-chr1:46595927..46599001,3	K562	blood:

Variant related genes	Relation type
ENSG00000227857	TF binding region
PIK3R3	TF binding region
ENSG00000111669	Chromatin interaction
ENSG00000132128	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000203875	Chromatin interaction
ENSG00000204439	Chromatin interaction
ENSG00000159592	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000086015	Chromatin interaction
ENSG00000171357	Chromatin interaction
ENSG00000173660	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000159596	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1085242	0.82[ASN][1000 genomes]
rs1085244	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10890383	0.82[EUR][1000 genomes]
rs11211251	0.82[ASN][1000 genomes]
rs11211252	0.82[ASN][1000 genomes]
rs1707304	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1707308	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1707321	0.82[ASN][1000 genomes]
rs1707333	0.84[ASN][1000 genomes]
rs1707334	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1707335	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1707340	0.82[ASN][1000 genomes]
rs1768803	0.86[ASN][1000 genomes]
rs1768816	0.82[ASN][1000 genomes]
rs2486445	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2486447	0.84[ASN][1000 genomes]
rs4660342	0.80[ASN][1000 genomes]
rs4660910	0.84[ASN][1000 genomes]
rs4660911	0.86[ASN][1000 genomes]
rs6662641	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6675726	0.87[ASN][1000 genomes]
rs785464	0.83[ASN][1000 genomes]
rs785471	0.82[ASN][1000 genomes]
rs785472	0.82[ASN][1000 genomes]
rs785473	0.82[ASN][1000 genomes]
rs785481	0.83[ASN][1000 genomes]
rs785482	0.80[ASN][1000 genomes]
rs785485	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785488	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785489	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785491	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785492	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785494	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785495	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs785498	0.87[ASN][1000 genomes]
rs785502	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs785503	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs785508	0.80[ASN][1000 genomes]
rs785509	0.80[ASN][1000 genomes]
rs785511	0.83[ASN][1000 genomes]
rs785513	0.82[ASN][1000 genomes]
rs785520	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs809774	0.84[ASN][1000 genomes]
rs809775	0.84[ASN][1000 genomes]
rs9429094	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9429183	0.82[ASN][1000 genomes]
rs9429189	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs1355642	CCDC163P	cis	Heart Left Ventricle	GTEx
rs1355642	CCDC163P	cis	Artery Aorta	GTEx
rs1355642	CCDC163P	cis	Esophagus Mucosa	GTEx
rs1355642	CCDC163P	cis	lung	GTEx
rs1355642	CCDC163P	cis	Stomach	GTEx
rs1355642	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs1355642	CCDC163P	cis	Esophagus Muscularis	GTEx
rs1355642	MAST2	cis	Artery Aorta	GTEx
rs1355642	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs1355642	CCDC163P	cis	Artery Tibial	GTEx
rs1355642	CCDC163P	cis	Muscle Skeletal	GTEx
rs1355642	CCDC163P	cis	Thyroid	GTEx
rs1355642	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs1355642	CCDC163P	cis	Whole Blood	GTEx
rs1355642	CCDC163P	cis	Adipose Subcutaneous	GTEx
rs1355642	MAST2	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46594000-46599000	Active TSS	Right Ventricle	heart
2	chr1:46594000-46599200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:46594000-46599200	Active TSS	Psoas Muscle	Psoas
4	chr1:46594000-46599400	Active TSS	Left Ventricle	heart
5	chr1:46594600-46599200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:46594600-46599400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:46594800-46599200	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr1:46594800-46599400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:46595000-46599200	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr1:46595200-46599200	Active TSS	Colon Smooth Muscle	Colon
11	chr1:46595200-46599200	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:46595200-46599400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:46595200-46599400	Active TSS	Fetal Heart	heart
14	chr1:46595200-46599400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:46595200-46599600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:46595400-46599000	Active TSS	Duodenum Mucosa	Duodenum
17	chr1:46595400-46599000	Active TSS	HMEC	breast
18	chr1:46595400-46599000	Active TSS	K562	blood
19	chr1:46595400-46599200	Active TSS	Fetal Brain Male	brain
20	chr1:46595400-46599200	Active TSS	Fetal Lung	lung
21	chr1:46595400-46599200	Active TSS	NH-A	brain
22	chr1:46595400-46599400	Active TSS	Brain Anterior Caudate	brain
23	chr1:46595400-46599600	Active TSS	Fetal Kidney	kidney
24	chr1:46595600-46599200	Active TSS	Brain Hippocampus Middle	brain
25	chr1:46595600-46599200	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr1:46595600-46599200	Active TSS	Fetal Brain Female	brain
27	chr1:46595600-46599200	Active TSS	GM12878-XiMat	blood
28	chr1:46595600-46599200	Active TSS	Hela-S3	cervix
29	chr1:46595600-46599400	Active TSS	Brain Angular Gyrus	brain
30	chr1:46595800-46599000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr1:46595800-46599000	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:46595800-46599000	Active TSS	Osteobl	bone
33	chr1:46595800-46599200	Active TSS	Fetal Muscle Leg	muscle
34	chr1:46595800-46599200	Active TSS	Fetal Stomach	stomach
35	chr1:46595800-46599200	Active TSS	Ovary	ovary
36	chr1:46595800-46599200	Active TSS	NHLF	lung
37	chr1:46595800-46599400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:46595800-46599400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:46595800-46599600	Active TSS	HSMMtube	muscle
40	chr1:46596000-46599000	Active TSS	HSMM	muscle
41	chr1:46596000-46599200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:46596000-46599200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:46596000-46599600	Active TSS	Fetal Intestine Large	intestine
44	chr1:46596000-46599600	Active TSS	Fetal Muscle Trunk	muscle
45	chr1:46596200-46599000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr1:46596200-46599200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:46596200-46599200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:46596200-46599200	Active TSS	Brain Substantia Nigra	brain
49	chr1:46596200-46599200	Active TSS	Rectal Smooth Muscle	rectum
50	chr1:46596200-46599400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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