Variant report

Variant	rs999418
Chromosome Location	chr1:153600124-153600125
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:426)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:426 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:153600080-153600230	GM12801	blood:	n/a	n/a
2	CTCF	chr1:153600120-153600270	HA-sp	spinal cord:	n/a	n/a
3	TAF1	chr1:153599654-153600298	Hela-S3	cervix:	n/a	n/a
4	ELF1	chr1:153599292-153600415	MCF-7	breast:	n/a	n/a
5	MYC	chr1:153599839-153600190	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr1:153600100-153600250	HMEC	breast:	n/a	n/a
7	TCF12	chr1:153599182-153600464	A549	lung:	n/a	n/a
8	CTCF	chr1:153600081-153600293	LNCaP	prostate:	n/a	n/a
9	CTCF	chr1:153600060-153600210	NHDF-neo	bronchial:	n/a	n/a
10	ZBTB7A	chr1:153600056-153600330	HepG2	liver:	n/a	chr1:153600154-153600163
11	POLR2A	chr1:153599446-153600166	A549	lung:	n/a	n/a
12	CTCF	chr1:153600080-153600230	GM12868	blood:	n/a	n/a
13	MYBL2	chr1:153599687-153600183	HepG2	liver:	n/a	n/a
14	CTCFL	chr1:153600017-153600257	K562	blood:	n/a	n/a
15	RAD21	chr1:153599929-153600333	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr1:153600041-153600205	SK-N-SH_RA	brain:	n/a	n/a
17	REST	chr1:153599514-153600143	A549	lung:	n/a	n/a
18	SMC3	chr1:153600037-153600229	GM12878	blood:	n/a	n/a
19	CTCF	chr1:153600080-153600230	GM12867	blood:	n/a	n/a
20	E2F4	chr1:153599878-153600232	MCF10A-Er-Src	breast:	n/a	n/a
21	MYBL2	chr1:153599642-153600294	HepG2	liver:	n/a	n/a
22	ZNF384	chr1:153599385-153600472	K562	blood:	n/a	n/a
23	ZBTB7A	chr1:153599183-153600573	ECC-1	luminal epithelium:	n/a	chr1:153600154-153600163
24	RAD21	chr1:153600035-153600221	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:153599381-153600254	K562	blood:	n/a	n/a
26	POLR2A	chr1:153599415-153600250	GM12892	blood:	n/a	n/a
27	MXI1	chr1:153599519-153600125	K562	blood:	n/a	n/a
28	ZBTB7A	chr1:153599943-153600636	K562	blood:	n/a	chr1:153600154-153600163
29	POLR2A	chr1:153599307-153600336	ProgFib	skin:	n/a	n/a
30	CTCF	chr1:153599904-153600371	A549	lung:	n/a	n/a
31	MAX	chr1:153599302-153600381	ECC-1	luminal epithelium:	n/a	n/a
32	SRF	chr1:153599260-153600305	MCF-7	breast:	n/a	n/a
33	CTCF	chr1:153600120-153600270	NB4	blood:	n/a	n/a
34	GTF2B	chr1:153599532-153600186	K562	blood:	n/a	n/a
35	RAD21	chr1:153599953-153600311	HepG2	liver:	n/a	n/a
36	CTCF	chr1:153600020-153600170	GM12871	blood:	n/a	n/a
37	FOXA1	chr1:153599905-153600283	T-47D	breast:	n/a	n/a
38	RAD21	chr1:153599454-153600466	A549	lung:	n/a	n/a
39	ELF1	chr1:153599774-153600315	A549	lung:	n/a	n/a
40	ATF2	chr1:153599873-153600278	H1-hESC	embryonic stem cell:	n/a	n/a
41	ZBTB33	chr1:153599596-153600356	HCT-116	colon:	n/a	n/a
42	MAX	chr1:153599353-153600326	K562	blood:	n/a	n/a
43	CTCF	chr1:153600060-153600210	AG10803	skin:	n/a	n/a
44	YY1	chr1:153599419-153600351	ECC-1	luminal epithelium:	n/a	n/a
45	CTCF	chr1:153600080-153600230	HUVEC	blood vessel:	n/a	n/a
46	CEBPB	chr1:153599430-153600218	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr1:153599058-153600390	HUVEC	blood vessel:	n/a	n/a
48	MAZ	chr1:153599536-153600370	HepG2	liver:	n/a	n/a
49	ELF1	chr1:153599723-153600210	K562	blood:	n/a	n/a
50	RCOR1	chr1:153599368-153600400	Hela-S3	cervix:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153599385..153600186-chr6:26285196..26286148,2	Hela-S3	cervix:
2	chr1:153599562..153600368-chr3:42622842..42623637,2	Hela-S3	cervix:
3	chr1:153599949..153601639-chr1:153935071..153937718,2	MCF-7	breast:
4	chr1:153505870..153508233-chr1:153598440..153600666,2	MCF-7	breast:
5	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
6	chr1:153598208..153601029-chr1:153962097..153964477,2	K562	blood:
7	chr1:153599788..153602388-chr1:153699187..153702024,4	MCF-7	breast:
8	chr1:153599101..153601090-chr1:153642486..153644716,4	MCF-7	breast:
9	chr1:153515275..153518447-chr1:153598676..153601896,4	MCF-7	breast:
10	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
11	chr1:153597855..153601076-chr1:153629883..153633781,4	MCF-7	breast:
12	chr1:153599500..153600347-chr2:10952822..10953337,2	Hela-S3	cervix:
13	chr1:153599526..153600299-chr7:45018463..45019401,2	Hela-S3	cervix:
14	chr1:153598241..153600189-chr1:153949006..153951530,2	MCF-7	breast:
15	chr1:153599605..153601359-chr1:153938449..153940087,2	MCF-7	breast:
16	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:
17	chr1:153599321..153600251-chr9:134269301..134270091,2	Hela-S3	cervix:
18	chr1:153599154..153601344-chr1:153747056..153749212,2	MCF-7	breast:
19	chr1:153585027..153585563-chr1:153599590..153600245,2	Hela-S3	cervix:
20	chr1:153580232..153580795-chr1:153599847..153600360,2	MCF-7	breast:
21	chr1:153538054..153540599-chr1:153598556..153600339,3	K562	blood:
22	chr1:153580167..153581037-chr1:153599715..153600388,2	MCF-7	breast:
23	chr1:153598392..153603036-chr1:153933813..153937554,5	MCF-7	breast:
24	chr1:153599607..153601795-chr12:120727965..120730762,2	MCF-7	breast:

No data

Variant related genes	Relation type
S100A1	TF binding region
S100A13	TF binding region
ENSG00000136286	Chromatin interaction
ENSG00000130723	Chromatin interaction
ENSG00000143570	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000143553	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000273026	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000143870	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000143578	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000143621	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1046381	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10797056	0.81[EUR][1000 genomes]
rs10908746	0.81[EUR][1000 genomes]
rs1128894	0.81[EUR][1000 genomes]
rs11497739	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11548102	0.96[ASN][1000 genomes]
rs11548103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11548104	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12564925	0.81[EUR][1000 genomes]
rs1411273	0.90[EUR][1000 genomes]
rs1810836	0.80[EUR][1000 genomes]
rs1888115	0.81[EUR][1000 genomes]
rs2274739	0.81[EUR][1000 genomes]
rs2274740	0.81[EUR][1000 genomes]
rs28379831	0.81[EUR][1000 genomes]
rs28380060	0.81[EUR][1000 genomes]
rs28416529	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28518786	0.81[ASN][1000 genomes]
rs28580554	0.81[EUR][1000 genomes]
rs28700217	0.81[EUR][1000 genomes]
rs28754733	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35760493	0.97[ASN][1000 genomes]
rs3790411	0.89[EUR][1000 genomes]
rs3790412	0.81[EUR][1000 genomes]
rs3806233	0.91[ASN][1000 genomes]
rs3818632	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3828031	0.81[EUR][1000 genomes]
rs4072425	0.96[ASN][1000 genomes]
rs4845557	0.81[EUR][1000 genomes]
rs7934	0.81[EUR][1000 genomes]
rs913860	0.81[EUR][1000 genomes]
rs913861	0.81[EUR][1000 genomes]
rs9330298	0.96[ASN][1000 genomes]
rs9330299	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9330300	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9330301	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9660679	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9699949	0.94[ASN][1000 genomes]
rs9700179	0.92[ASN][1000 genomes]
rs9700928	0.96[ASN][1000 genomes]
rs9726753	0.96[ASN][1000 genomes]
rs9729773	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9792913	0.96[ASN][1000 genomes]
rs9792963	0.96[ASN][1000 genomes]
rs9792967	0.96[ASN][1000 genomes]
rs9793310	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs985242	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs999418	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs999418	RP1-178F15.4	cis	lung	GTEx
rs999418	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs999418	RP1-178F15.4	cis	Artery Tibial	GTEx
rs999418	S100A14	cis	Thyroid	GTEx
rs999418	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs999418	RP1-178F15.4	cis	Artery Aorta	GTEx
rs999418	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs999418	CHTOP	cis	Muscle Skeletal	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153596800-153600400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:153597600-153600600	Enhancers	GM12878-XiMat	blood
3	chr1:153597800-153600800	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:153598200-153603600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:153598400-153600200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:153598400-153600200	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr1:153598400-153600400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:153598400-153600400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:153598600-153600200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:153598600-153600400	Flanking Active TSS	Colonic Mucosa	Colon
11	chr1:153598600-153600400	Flanking Active TSS	Duodenum Mucosa	Duodenum
12	chr1:153598600-153600400	Flanking Active TSS	HUVEC	blood vessel
13	chr1:153598600-153601800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr1:153598800-153600200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:153598800-153600200	Flanking Active TSS	Placenta	Placenta
16	chr1:153598800-153600200	Flanking Active TSS	Pancreas	Pancrea
17	chr1:153598800-153600200	Flanking Active TSS	Right Ventricle	heart
18	chr1:153598800-153600400	Flanking Active TSS	Brain Angular Gyrus	brain
19	chr1:153598800-153600400	Flanking Active TSS	Fetal Muscle Trunk	muscle
20	chr1:153598800-153601400	Flanking Active TSS	Brain Hippocampus Middle	brain
21	chr1:153598800-153601400	Flanking Active TSS	K562	blood
22	chr1:153598800-153602200	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr1:153598800-153602400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
24	chr1:153599000-153600200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:153599000-153600200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:153599000-153600200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr1:153599000-153600200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
28	chr1:153599000-153600200	Flanking Active TSS	Fetal Intestine Small	intestine
29	chr1:153599000-153600200	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:153599000-153600200	Flanking Active TSS	Fetal Muscle Leg	muscle
31	chr1:153599000-153600200	Flanking Active TSS	Fetal Stomach	stomach
32	chr1:153599000-153600200	Active TSS	NHDF-Ad	bronchial
33	chr1:153599000-153600400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:153599000-153600400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr1:153599200-153600200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr1:153599200-153600200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:153599200-153600200	Active TSS	Fetal Kidney	kidney
38	chr1:153599200-153600200	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:153599200-153600400	Flanking Active TSS	NHEK	skin
40	chr1:153599400-153600200	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr1:153599400-153600200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:153599400-153600200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:153599400-153600200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:153599400-153600200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:153599400-153600200	Active TSS	Sigmoid Colon	Sigmoid Colon
46	chr1:153599400-153600200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr1:153599400-153600400	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:153599400-153600400	Enhancers	Primary B cells from cord blood	blood
49	chr1:153599400-153600800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:153599600-153600200	Active TSS	H1 Cell Line	embryonic stem cell

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