Variant report

Variant	rs1913117
Chromosome Location	chr1:150552534-150552535
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	POLR2A	chr1:150550789-150552538	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr1:150546850-150552818	GM12878	blood:	n/a	n/a
3	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
4	POLR2A	chr1:150551528-150552844	SK-N-SH	brain:	n/a	n/a
5	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
6	ARID3A	chr1:150551901-150552649	HepG2	liver:	n/a	n/a
7	CEBPB	chr1:150550798-150552753	MCF-7	breast:	n/a	n/a
8	POLR2A	chr1:150552245-150552692	GM12892	blood:	n/a	n/a
9	CHD2	chr1:150551012-150552573	Hela-S3	cervix:	n/a	n/a
10	RELA	chr1:150551862-150552581	GM18526	blood:	n/a	n/a
11	RELA	chr1:150551842-150552691	GM12892	blood:	n/a	n/a
12	ELF1	chr1:150551591-150552716	HCT-116	colon:	n/a	chr1:150552014-150552023 chr1:150552070-150552079 chr1:150552067-150552080 chr1:150552017-150552026
13	SRF	chr1:150550634-150552910	MCF-7	breast:	n/a	chr1:150551994-150552009 chr1:150552167-150552185 chr1:150552169-150552187 chr1:150552172-150552189 chr1:150552170-150552185
14	POLR2A	chr1:150550237-150552750	GM19099	blood:	n/a	n/a
15	TBL1XR1	chr1:150551571-150552735	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:150546864-150552806	GM18505	blood:	n/a	n/a
17	SIN3AK20	chr1:150550672-150552836	HCT-116	colon:	n/a	n/a
18	ZKSCAN1	chr1:150550788-150552743	Hela-S3	cervix:	n/a	n/a
19	TAF1	chr1:150552271-150552586	PFSK-1	brain:	n/a	n/a
20	SIN3AK20	chr1:150550729-150552540	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:150551146-150552596	Gliobla	brain:	n/a	n/a
22	CREB1	chr1:150550768-150552671	H1-hESC	embryonic stem cell:	n/a	n/a
23	RELA	chr1:150550817-150552622	GM18951	blood:	n/a	n/a
24	POLR2A	chr1:150550168-150552761	HUVEC	blood vessel:	n/a	n/a
25	REST	chr1:150549530-150553038	H1-neurons	neurons:	n/a	chr1:150552093-150552101
26	FOSL2	chr1:150550462-150552671	A549	lung:	n/a	chr1:150551163-150551174
27	TEAD4	chr1:150549117-150552737	K562	blood:	n/a	n/a
28	ELK1	chr1:150550742-150552648	Hela-S3	cervix:	n/a	n/a
29	EP300	chr1:150551822-150552698	K562	blood:	n/a	chr1:150552342-150552358 chr1:150552015-150552024 chr1:150552069-150552083
30	ELF1	chr1:150551580-150552726	HCT-116	colon:	n/a	chr1:150552014-150552023 chr1:150552070-150552079 chr1:150552067-150552080 chr1:150552017-150552026
31	RELA	chr1:150551842-150552634	GM19099	blood:	n/a	n/a
32	REST	chr1:150551740-150552555	HepG2	liver:	n/a	chr1:150552093-150552101
33	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
34	POLR2A	chr1:150550660-150553289	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:150550505-150553020	K562	blood:	n/a	n/a
36	POLR2A	chr1:150538889-150552727	K562	blood:	n/a	n/a
37	TAF1	chr1:150550852-150552627	ECC-1	luminal epithelium:	n/a	n/a
38	POLR2A	chr1:150549143-150552715	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr1:150551016-150552743	K562	blood:	n/a	n/a
40	PML	chr1:150550856-150552762	MCF-7	breast:	n/a	n/a
41	POLR2A	chr1:150550648-150552609	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr1:150550177-150552629	HUVEC	blood vessel:	n/a	n/a
43	CEBPD	chr1:150550662-150552610	K562	blood:	n/a	n/a
44	POLR2A	chr1:150546598-150553153	U87	brain:	n/a	n/a
45	POLR2A	chr1:150552271-150552658	HL-60	blood:	n/a	n/a
46	POLR2A	chr1:150546807-150552855	SK-N-SH	brain:	n/a	n/a
47	MTA3	chr1:150552264-150552848	GM12878	blood:	n/a	n/a
48	PML	chr1:150551420-150552666	K562	blood:	n/a	n/a
49	POLR2A	chr1:150550241-150552766	GM12878	blood:	n/a	n/a
50	IRF1	chr1:150551813-150552596	K562	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	chr1:150552019..150552561-chr20:43594621..43595161,2	NB4	blood:
5	chr1:150548752..150555486-chr1:150599368..150605834,15	MCF-7	breast:
6	chr1:150336951..150339274-chr1:150551327..150552882,2	K562	blood:
7	chr1:150547577..150553391-chr1:150562900..150573800,12	MCF-7	breast:
8	chr1:150551507..150553628-chr1:150668472..150670953,2	K562	blood:
9	chr1:150550567..150552845-chr1:151042071..151045056,2	MCF-7	breast:
10	chr1:150551996..150552577-chr15:74833132..74834047,2	Hela-S3	cervix:
11	chr1:150550164..150555275-chr1:150782862..150788394,7	MCF-7	breast:
12	chr1:150550706..150553008-chr1:150788888..150791389,2	K562	blood:
13	chr1:150550605..150553329-chr1:151136705..151138908,2	K562	blood:
14	chr1:150458615..150462130-chr1:150550221..150553114,4	K562	blood:
15	chr1:150551078..150552936-chr1:150667990..150671349,4	K562	blood:
16	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
17	chr1:150551863..150552672-chr2:43453330..43454322,2	MCF-7	breast:
18	chr1:150521298..150527553-chr1:150548198..150553572,10	MCF-7	breast:
19	chr1:150550535..150554049-chr1:150976755..150981799,6	K562	blood:
20	chr1:150552057..150552895-chr7:139025854..139026496,2	Hela-S3	cervix:
21	chr1:150551989..150552685-chr17:15554385..15554952,2	MCF-7	breast:
22	chr1:150548124..150553459-chr1:150571951..150579395,15	MCF-7	breast:
23	chr1:150551961..150552659-chr6:35888288..35889046,2	HCT-116	colon:
24	chr1:150551378..150553300-chr1:150944488..150946159,2	MCF-7	breast:
25	chr1:150459417..150461989-chr1:150549858..150552620,3	MCF-7	breast:
26	chr1:150549378..150552816-chr1:151028901..151032004,3	K562	blood:
27	chr1:150533865..150534729-chr1:150551971..150552548,2	Hela-S3	cervix:

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

Variant related genes	Relation type
MCL1	TF binding region
ENSG00000203804	Chromatin interaction
ENSG00000266261	Chromatin interaction
ENSG00000227477	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000213190	Chromatin interaction
ENSG00000143409	Chromatin interaction
ENSG00000101109	Chromatin interaction
ENSG00000143420	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000143437	Chromatin interaction
ENSG00000264553	Chromatin interaction
ENSG00000231073	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000152518	Chromatin interaction
ENSG00000096063	Chromatin interaction
ENSG00000200175	Chromatin interaction
ENSG00000253047	Chromatin interaction
ENSG00000143457	Chromatin interaction
ENSG00000179361	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10305729	1.00[AMR][1000 genomes]
rs1543089	1.00[ASW][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16837742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1913116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34896634	1.00[AFR][1000 genomes];1.00[AMR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1913117	HBD	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 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	chr1:150548800-150552600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:150549000-150552600	Active TSS	Stomach Mucosa	stomach
6	chr1:150549000-150553000	Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr1:150549200-150553000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:150549600-150552800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:150549800-150552600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:150549800-150552600	Active TSS	Small Intestine	intestine
11	chr1:150549800-150552800	Active TSS	Psoas Muscle	Psoas
12	chr1:150550000-150552600	Active TSS	Brain Angular Gyrus	brain
13	chr1:150550000-150552600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:150550000-150552600	Active TSS	Brain Substantia Nigra	brain
15	chr1:150550000-150552600	Active TSS	Fetal Brain Female	brain
16	chr1:150550000-150552800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:150550000-150552800	Active TSS	Lung	lung
18	chr1:150550000-150552800	Active TSS	Pancreas	Pancrea
19	chr1:150550000-150553000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:150550200-150552800	Active TSS	Liver	Liver
21	chr1:150550400-150552600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:150550400-150552800	Active TSS	Right Ventricle	heart
23	chr1:150550600-150552600	Active TSS	Brain Cingulate Gyrus	brain
24	chr1:150550800-150553000	Active TSS	GM12878-XiMat	blood
25	chr1:150551000-150552600	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:150551000-150552600	Active TSS	Fetal Muscle Trunk	muscle
27	chr1:150551000-150553000	Active TSS	Colonic Mucosa	Colon
28	chr1:150551000-150553000	Active TSS	HSMM	muscle
29	chr1:150551200-150552600	Active TSS	K562	blood
30	chr1:150551200-150553000	Active TSS	Thymus	Thymus
31	chr1:150551400-150552600	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr1:150551400-150552600	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr1:150551400-150552600	Active TSS	NHDF-Ad	bronchial
34	chr1:150551400-150552800	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:150551400-150552800	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr1:150551400-150553000	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:150551400-150553200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:150551400-150553200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:150551600-150552600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:150551600-150552600	Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr1:150551600-150552600	Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr1:150551600-150552600	Active TSS	Esophagus	oesophagus
43	chr1:150551600-150552600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:150551600-150552600	Active TSS	Fetal Stomach	stomach
45	chr1:150551600-150552800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:150551600-150552800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:150551600-150552800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
48	chr1:150551600-150552800	Active TSS	Left Ventricle	heart
49	chr1:150551800-150552600	Active TSS	Colon Smooth Muscle	Colon
50	chr1:150551800-150553000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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