Variant report

Variant	rs10494162
Chromosome Location	chr1:114473083-114473084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:143)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:143 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT1	chr1:114472731-114473324	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:114470792-114473521	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:114470836-114473396	K562	blood:	n/a	n/a
4	TBL1XR1	chr1:114472549-114474429	K562	blood:	n/a	n/a
5	POLR2A	chr1:114471482-114473538	H1-neurons	neurons:	n/a	n/a
6	POLR2A	chr1:114471073-114473562	GM12878	blood:	n/a	n/a
7	MXI1	chr1:114470648-114473883	SK-N-SH	brain:	n/a	n/a
8	GATA1	chr1:114472688-114474537	PBDE	blood:	n/a	chr1:114474064-114474072 chr1:114474379-114474388 chr1:114473637-114473648
9	POLR2A	chr1:114471538-114473494	K562	blood:	n/a	n/a
10	POLR2A	chr1:114471293-114473102	GM18526	blood:	n/a	n/a
11	ELF1	chr1:114471516-114473429	K562	blood:	n/a	chr1:114472196-114472208 chr1:114472308-114472320
12	TAF1	chr1:114472659-114473090	Hela-S3	cervix:	n/a	n/a
13	RUNX3	chr1:114472639-114473549	GM12878	blood:	n/a	n/a
14	SIN3A	chr1:114471570-114473630	H1-hESC	embryonic stem cell:	n/a	chr1:114472939-114472947 chr1:114472289-114472302
15	MXI1	chr1:114471415-114473383	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:114472646-114473412	GM12891	blood:	n/a	n/a
17	MAZ	chr1:114471330-114474073	IMR90	lung:	n/a	chr1:114472800-114472810 chr1:114473592-114473601
18	POLR2A	chr1:114471568-114473374	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr1:114472743-114473398	Hela-S3	cervix:	n/a	n/a
20	GABPA	chr1:114470713-114473802	MCF-7	breast:	n/a	chr1:114472320-114472329
21	POLR2A	chr1:114470824-114473119	Raji	blood:	n/a	n/a
22	SMARCC1	chr1:114471417-114473585	Hela-S3	cervix:	n/a	n/a
23	TBP	chr1:114470891-114473736	K562	blood:	n/a	n/a
24	POLR2A	chr1:114471669-114473531	NB4	blood:	n/a	n/a
25	CUX1	chr1:114472799-114473105	K562	blood:	n/a	n/a
26	POLR2A	chr1:114470515-114473570	K562	blood:	n/a	n/a
27	ZNF384	chr1:114471741-114474455	K562	blood:	n/a	chr1:114472880-114472888
28	CHD1	chr1:114471322-114475053	IMR90	lung:	n/a	chr1:114472166-114472176
29	TEAD4	chr1:114472423-114474647	K562	blood:	n/a	n/a
30	PML	chr1:114471482-114473795	K562	blood:	n/a	n/a
31	MTA3	chr1:114472723-114473447	GM12878	blood:	n/a	n/a
32	POLR2A	chr1:114472656-114473480	GM12878	blood:	n/a	n/a
33	MAX	chr1:114471209-114473560	NB4	blood:	n/a	chr1:114472800-114472810
34	POLR2A	chr1:114472454-114473471	GM12891	blood:	n/a	n/a
35	WRNIP1	chr1:114472923-114473531	GM12878	blood:	n/a	n/a
36	CTCF	chr1:114473080-114473230	AG04450	lung:	n/a	n/a
37	ELK1	chr1:114472828-114473685	K562	blood:	n/a	n/a
38	MAX	chr1:114472652-114473452	GM12878	blood:	n/a	chr1:114472800-114472810
39	SRF	chr1:114470588-114473873	MCF-7	breast:	n/a	chr1:114472196-114472206 chr1:114471150-114471165
40	RCOR1	chr1:114472733-114473479	GM12878	blood:	n/a	n/a
41	POLR2A	chr1:114471671-114473336	K562	blood:	n/a	n/a
42	POLR2A	chr1:114470886-114473746	MCF10A-Er-Src	breast:	n/a	n/a
43	BHLHE40	chr1:114471029-114473735	GM12878	blood:	n/a	chr1:114472288-114472304 chr1:114472299-114472315
44	MXI1	chr1:114472554-114473860	K562	blood:	n/a	n/a
45	BHLHE40	chr1:114472545-114473703	K562	blood:	n/a	n/a
46	CHD2	chr1:114471283-114473232	K562	blood:	n/a	chr1:114472166-114472176
47	ZMIZ1	chr1:114471746-114473448	K562	blood:	n/a	n/a
48	MAX	chr1:114471580-114473417	Hela-S3	cervix:	n/a	chr1:114472800-114472810
49	SMC3	chr1:114472637-114473425	Hela-S3	cervix:	n/a	chr1:114472804-114472814
50	POLR2A	chr1:114472580-114473686	GM12878	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114447832..114448433-chr1:114472824..114473410,2	Hela-S3	cervix:
2	chr1:114471153..114473640-chr17:59476771..59478545,2	MCF-7	breast:
3	chr1:108289707..108293879-chr1:114470865..114473423,4	MCF-7	breast:
4	chr1:114472004..114474163-chr17:56707756..56710387,2	MCF-7	breast:
5	chr1:114472262..114473380-chr1:114505771..114506776,3	MCF-7	breast:
6	chr1:114471318..114473682-chr17:59475992..59478676,2	MCF-7	breast:
7	chr1:114472848..114474894-chr20:52685682..52687660,2	MCF-7	breast:
8	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
9	chr1:114299235..114302663-chr1:114470274..114473459,3	K562	blood:
10	chr1:114300069..114302951-chr1:114469985..114474355,4	MCF-7	breast:
11	chr1:114447415..114448376-chr1:114471694..114473083,5	MCF-7	breast:
12	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
13	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
14	chr1:114301163..114303418-chr1:114471834..114473459,2	K562	blood:
15	chr1:114469554..114476691-chr1:114493097..114498363,7	MCF-7	breast:
16	chr1:114300200..114301915-chr1:114470901..114473894,2	MCF-7	breast:
17	chr1:108741161..108744200-chr1:114469971..114473274,3	MCF-7	breast:
18	chr1:114447369..114448385-chr1:114471257..114473158,18	MCF-7	breast:
19	chr1:114352160..114355349-chr1:114470537..114474785,4	K562	blood:
20	chr1:114439933..114443921-chr1:114470851..114474658,5	K562	blood:
21	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:
22	chr1:114471506..114473104-chr1:114522240..114523784,2	K562	blood:

No data

Variant related genes	Relation type
HIPK1	TF binding region
ENSG00000235527	TF binding region
ENSG00000134215	Chromatin interaction
ENSG00000116774	Chromatin interaction
ENSG00000260879	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000085491	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10108	0.82[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10494163	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs11102703	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11102706	0.93[ASN][1000 genomes]
rs11102707	1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11102708	0.92[ASN][1000 genomes]
rs11102709	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12060750	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12125546	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12127377	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12129050	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1217444	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503832	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1553449	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553450	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17852555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[ASN][1000 genomes]
rs1910485	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1985435	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1985436	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41302825	0.91[ASN][1000 genomes]
rs6537800	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6669370	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6674384	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7364	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs7519860	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7546851	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs756493	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs878129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv3349186	chr1:114471379-114473627	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10494162	DCLRE1B	cis	lesional skin	skin_eQTL
rs10494162	DCLRE1B	cis	uninvolved skin	skin_eQTL
rs10494162	DCLRE1B	Cis_1M	lymphoblastoid	RTeQTL
rs10494162	DCLRE1B	cis	normal skin	skin_eQTL
rs10494162	DCLRE1B	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114470800-114473400	Active TSS	Fetal Intestine Large	intestine
2	chr1:114470800-114473400	Active TSS	Fetal Intestine Small	intestine
3	chr1:114470800-114474000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:114470800-114474200	Active TSS	Aorta	Aorta
5	chr1:114470800-114476200	Active TSS	Thymus	Thymus
6	chr1:114471000-114473200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:114471000-114473200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:114471000-114473400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:114471000-114473400	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:114471000-114473400	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr1:114471000-114473400	Active TSS	Stomach Mucosa	stomach
12	chr1:114471000-114473400	Bivalent/Poised TSS	HepG2	liver
13	chr1:114471000-114473600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:114471000-114473600	Active TSS	Ovary	ovary
15	chr1:114471000-114473600	Active TSS	HSMM	muscle
16	chr1:114471000-114473800	Active TSS	Colonic Mucosa	Colon
17	chr1:114471000-114473800	Active TSS	NHDF-Ad	bronchial
18	chr1:114471000-114474000	Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr1:114471000-114474200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:114471000-114474200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:114471000-114474800	Active TSS	GM12878-XiMat	blood
22	chr1:114471200-114473200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:114471200-114473200	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr1:114471200-114473400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:114471200-114473400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:114471200-114473400	Active TSS	Placenta Amnion	Placenta Amnion
27	chr1:114471200-114473600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr1:114471200-114473600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:114471200-114473600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr1:114471200-114473600	Active TSS	Fetal Muscle Trunk	muscle
31	chr1:114471200-114473600	Active TSS	Lung	lung
32	chr1:114471200-114473600	Active TSS	Pancreas	Pancrea
33	chr1:114471200-114473800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr1:114471200-114474000	Active TSS	K562	blood
35	chr1:114471200-114474200	Active TSS	Sigmoid Colon	Sigmoid Colon
36	chr1:114471200-114474400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:114471200-114474800	Active TSS	Psoas Muscle	Psoas
38	chr1:114471400-114473200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:114471400-114473200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:114471400-114473200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:114471400-114473200	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr1:114471400-114473200	Active TSS	Brain Cingulate Gyrus	brain
43	chr1:114471400-114473200	Active TSS	Brain Germinal Matrix	brain
44	chr1:114471400-114473200	Active TSS	Colon Smooth Muscle	Colon
45	chr1:114471400-114473200	Active TSS	Fetal Heart	heart
46	chr1:114471400-114473200	Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:114471400-114473400	Active TSS	H1 Cell Line	embryonic stem cell
48	chr1:114471400-114473400	Active TSS	Small Intestine	intestine
49	chr1:114471400-114473600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:114471400-114473600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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