Variant report

Variant	rs3748631
Chromosome Location	chr1:222886588-222886589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:527)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:527 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:222886516-222886874	HepG2	liver:	n/a	chr1:222886651-222886660 chr1:222886649-222886663 chr1:222886665-222886674 chr1:222886649-222886660
2	TAF1	chr1:222885621-222886992	GM12878	blood:	n/a	n/a
3	SRF	chr1:222886347-222886818	GM12878	blood:	n/a	n/a
4	USF1	chr1:222885736-222886758	H1-hESC	embryonic stem cell:	n/a	n/a
5	YY1	chr1:222885690-222887002	K562	blood:	n/a	n/a
6	CTCF	chr1:222886540-222886690	GM12869	blood:	n/a	n/a
7	PML	chr1:222885681-222887057	K562	blood:	n/a	chr1:222886762-222886770
8	E2F6	chr1:222884665-222887010	K562	blood:	n/a	chr1:222886650-222886659 chr1:222885810-222885818
9	FOXP2	chr1:222886542-222886906	PFSK-1	brain:	n/a	n/a
10	POU2F2	chr1:222886402-222886862	GM12891	blood:	n/a	n/a
11	MYC	chr1:222886586-222886608	K562	blood:	n/a	n/a
12	MYC	chr1:222884615-222886950	K562	blood:	n/a	chr1:222886670-222886680
13	POLR2A	chr1:222886421-222887032	GM12878	blood:	n/a	n/a
14	EBF1	chr1:222886432-222887038	GM12878	blood:	n/a	n/a
15	TCF12	chr1:222885681-222887190	A549	lung:	n/a	n/a
16	POLR2A	chr1:222884479-222887260	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr1:222885564-222886959	U87	brain:	n/a	n/a
18	ATF3	chr1:222885891-222886814	A549	lung:	n/a	n/a
19	REST	chr1:222886447-222886894	K562	blood:	n/a	n/a
20	MAZ	chr1:222885773-222887381	GM12878	blood:	n/a	chr1:222886670-222886680
21	SRF	chr1:222886243-222886780	H1-hESC	embryonic stem cell:	n/a	n/a
22	MAX	chr1:222885725-222886961	MCF-7	breast:	n/a	chr1:222886670-222886680
23	E2F6	chr1:222886391-222886804	K562	blood:	n/a	chr1:222886650-222886659
24	MBD4	chr1:222886154-222887036	HepG2	liver:	n/a	n/a
25	SIN3A	chr1:222884727-222887390	H1-hESC	embryonic stem cell:	n/a	n/a
26	ZNF384	chr1:222885922-222886989	K562	blood:	n/a	n/a
27	REST	chr1:222886442-222886928	HepG2	liver:	n/a	n/a
28	BHLHE40	chr1:222886523-222886790	HepG2	liver:	n/a	n/a
29	SMC3	chr1:222885841-222886999	Hela-S3	cervix:	n/a	chr1:222886667-222886677
30	TAF1	chr1:222886578-222886854	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr1:222886351-222886968	HepG2	liver:	n/a	n/a
32	CHD2	chr1:222885977-222886947	H1-hESC	embryonic stem cell:	n/a	n/a
33	ELF1	chr1:222885733-222887068	SK-N-SH	brain:	n/a	n/a
34	USF1	chr1:222885734-222886851	ECC-1	luminal epithelium:	n/a	n/a
35	CREB1	chr1:222886421-222886913	H1-hESC	embryonic stem cell:	n/a	n/a
36	E2F4	chr1:222885528-222886840	MCF10A-Er-Src	breast:	n/a	chr1:222886650-222886659 chr1:222885810-222885818
37	ELF1	chr1:222885709-222887352	HCT-116	colon:	n/a	n/a
38	CTCF	chr1:222886500-222886650	GM12874	blood:	n/a	n/a
39	SRF	chr1:222886348-222886767	GM12878	blood:	n/a	n/a
40	MAX	chr1:222885713-222886982	ECC-1	luminal epithelium:	n/a	chr1:222886670-222886680
41	ATF2	chr1:222885936-222886837	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZMIZ1	chr1:222884806-222887257	K562	blood:	n/a	n/a
43	CREB1	chr1:222886415-222887018	A549	lung:	n/a	n/a
44	MYBL2	chr1:222885882-222887052	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:222885142-222887096	GM12892	blood:	n/a	n/a
46	EGR1	chr1:222886455-222886982	K562	blood:	n/a	chr1:222886650-222886659
47	YY1	chr1:222885701-222886806	H1-hESC	embryonic stem cell:	n/a	n/a
48	STAT1	chr1:222885827-222887019	GM12878	blood:	n/a	n/a
49	POLR2A	chr1:222884702-222887083	GM19193	blood:	n/a	n/a
50	HA-E2F1	chr1:222885346-222886877	Hela-S3	cervix:	n/a	chr1:222886650-222886659

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:222886563-222886613	HIPEpiC	eye:	n/a
2	chr1:222886563-222886613	IMR90	lung:	fetal
3	chr1:222886563-222886613	HepG2	liver:	n/a
4	chr1:222886563-222886613	NH-A	brain:	n/a
5	chr1:222886563-222886613	SKMC	muscle:	n/a
6	chr1:222886563-222886613	HEK293	kidney:	embryo
7	chr1:222886563-222886613	ProgFib	skin:	n/a
8	chr1:222886563-222886613	H1-hESC	embryonic stem cell:	embryo
9	chr1:222886563-222886613	RPTEC	kidney:	n/a
10	chr1:222886563-222886613	HAEpiC	amniotic membrane:	n/a
11	chr1:222886563-222886613	HPAEpiC	pulmonary alveolar:	n/a
12	chr1:222886563-222886613	NHBE	bronchial:	n/a
13	chr1:222886563-222886613	SK-N-MC	brain:	n/a
14	chr1:222886563-222886613	HCF	heart:	n/a
15	chr1:222886563-222886613	GM12878	blood:	n/a
16	chr1:222886563-222886613	LNCaP	prostate:	n/a
17	chr1:222886563-222886613	SK-N-SH_RA	brain:	n/a
18	chr1:222886563-222886613	HCM	heart:	n/a
19	chr1:222886563-222886613	HNPCEpiC	eye:	n/a
20	chr1:222886563-222886613	HL-60	blood:	n/a
21	chr1:222886563-222886613	GM19239	blood:	n/a
22	chr1:222886563-222886613	GM06990	blood:	n/a
23	chr1:222886563-222886613	HRPEpiC	eye:	n/a
24	chr1:222886563-222886613	Caco-2	colon:	n/a
25	chr1:222886563-222886613	ovcar-3	ovarian:	n/a
26	chr1:222886563-222886613	PrEC	prostate:	n/a
27	chr1:222886563-222886613	HCPEpiC	choroid plexus:	n/a
28	chr1:222886563-222886613	HUVEC	blood vessel:	n/a
29	chr1:222886563-222886613	HRCEpiC	kidney:	n/a
30	chr1:222886563-222886613	MCF-7	breast:	n/a
31	chr1:222886563-222886613	HMEC	breast:	n/a
32	chr1:222886563-222886613	AG04449	skin:	fetal
33	chr1:222886563-222886613	K562	blood:	n/a
34	chr1:222886563-222886613	HEEpiC	esophagus:	n/a
35	chr1:222886563-222886613	AG09319	gingival:	n/a
36	chr1:222886563-222886613	CMK	blood:	n/a
37	chr1:222886563-222886613	A549	lung:	n/a
38	chr1:222886563-222886613	Hepatocyte	liver:	n/a
39	chr1:222886563-222886613	NHDF-neo	bronchial:	n/a
40	chr1:222886563-222886613	AG10803	skin:	n/a
41	chr1:222886563-222886613	Hela-S3	cervix:	n/a
42	chr1:222886563-222886613	AG09309	skin:	n/a
43	chr1:222886563-222886613	HRE	kidney:	n/a
44	chr1:222886563-222886613	T-47D	breast:	n/a
45	chr1:222886563-222886613	BE2_C	brain:	n/a
46	chr1:222886563-222886613	PANC-1	pancreas:	n/a
47	chr1:222886563-222886613	MCF10A-Er-Src	breast:	n/a
48	chr1:222886563-222886613	GM12892	blood:	n/a
49	chr1:222886563-222886613	PFSK-1	brain:	n/a
50	chr1:222886563-222886613	U87	brain:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:222760324..222764721-chr1:222884429..222887789,6	K562	blood:
2	chr1:222814795..222819438-chr1:222884035..222887873,13	K562	blood:
3	chr1:222849453..222853444-chr1:222884619..222888596,6	K562	blood:
4	chr1:222837235..222840536-chr1:222884708..222887368,3	MCF-7	breast:
5	chr1:222886023..222886943-chr17:1552762..1553506,2	Hela-S3	cervix:
6	chr1:222886029..222886690-chr3:156878406..156878911,2	Hela-S3	cervix:
7	chr1:222817680..222819791-chr1:222885041..222887043,2	MCF-7	breast:
8	chr1:222886462..222887267-chr2:67624303..67624946,2	Hela-S3	cervix:
9	chr1:222789930..222793106-chr1:222884660..222888170,6	K562	blood:
10	chr1:222790149..222792584-chr1:222885363..222887404,2	K562	blood:
11	chr1:222885691..222887842-chr17:56707440..56710300,2	MCF-7	breast:
12	chr1:222886384..222887150-chr10:14880331..14880877,2	Hela-S3	cervix:
13	chr1:222762075..222764721-chr1:222883311..222887470,5	K562	blood:
14	chr1:222886239..222887225-chr7:12250816..12251369,2	Hela-S3	cervix:
15	chr1:222886479..222886979-chr6:27114337..27115178,2	Hela-S3	cervix:
16	chr1:222886038..222886696-chr10:101380647..101381633,2	Hela-S3	cervix:
17	chr1:222815622..222820703-chr1:222883498..222888165,14	K562	blood:

No data

Variant related genes	Relation type
RN7SL276P	TF binding region
AIDA	TF binding region
BROX	TF binding region
BROX	CpG island
RN7SL276P	CpG island
AIDA	CpG island
ENSG00000186063	Chromatin interaction
ENSG00000143498	Chromatin interaction
ENSG00000106460	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000154305	Chromatin interaction
ENSG00000185267	Chromatin interaction
ENSG00000143971	Chromatin interaction
ENSG00000260475	Chromatin interaction
ENSG00000225265	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000187522	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000229399	Chromatin interaction
ENSG00000167705	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10495200	1.00[CEU][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs11118971	1.00[ASN][1000 genomes]
rs12058171	0.89[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163431	1.00[ASN][1000 genomes]
rs17163437	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17163441	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474333	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17531063	0.84[AFR][1000 genomes]
rs17531300	0.94[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap]
rs17531468	0.84[AFR][1000 genomes]
rs17532610	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35684750	0.82[MEX][hapmap];0.81[EUR][1000 genomes]
rs35762933	0.82[MEX][hapmap];0.82[EUR][1000 genomes]
rs3748629	0.84[AFR][1000 genomes]
rs41424447	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124884	0.81[EUR][1000 genomes]
rs7520650	0.81[EUR][1000 genomes]
rs9286760	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441846	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9441936	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3748631	HHIPL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222883200-222887600	Active TSS	Brain Anterior Caudate	brain
2	chr1:222883800-222887400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:222883800-222887600	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr1:222883800-222887600	Active TSS	Fetal Kidney	kidney
5	chr1:222883800-222887600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr1:222883800-222887600	Active TSS	NHLF	lung
7	chr1:222883800-222887800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:222883800-222887800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:222883800-222888000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:222883800-222888000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:222884000-222887200	Active TSS	Brain Angular Gyrus	brain
12	chr1:222884000-222887400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:222884000-222887400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr1:222884000-222887600	Active TSS	H1 Cell Line	embryonic stem cell
15	chr1:222884000-222887600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:222884000-222887600	Active TSS	Fetal Intestine Small	intestine
17	chr1:222884000-222887600	Active TSS	Ovary	ovary
18	chr1:222884000-222887600	Active TSS	Right Atrium	heart
19	chr1:222884000-222887600	Active TSS	A549	lung
20	chr1:222884000-222887600	Active TSS	GM12878-XiMat	blood
21	chr1:222884000-222887600	Active TSS	HSMM	muscle
22	chr1:222884000-222887800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:222884000-222887800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:222884200-222887200	Active TSS	Hela-S3	cervix
25	chr1:222884200-222887200	Active TSS	NH-A	brain
26	chr1:222884200-222887400	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:222884200-222887400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr1:222884200-222887400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:222884200-222887400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr1:222884200-222887400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:222884200-222887400	Active TSS	HSMMtube	muscle
32	chr1:222884200-222887600	Active TSS	H9 Cell Line	embryonic stem cell
33	chr1:222884200-222887600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:222884200-222887600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:222884200-222887600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:222884200-222887600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:222884200-222887600	Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr1:222884200-222887600	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:222884200-222887600	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr1:222884200-222887600	Active TSS	Muscle Satellite Cultured Cells	--
41	chr1:222884200-222887600	Active TSS	Fetal Stomach	stomach
42	chr1:222884200-222887600	Active TSS	NHDF-Ad	bronchial
43	chr1:222884200-222888000	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr1:222884400-222887200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:222884400-222887200	Active TSS	Colon Smooth Muscle	Colon
46	chr1:222884400-222887200	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr1:222884400-222887200	Active TSS	HUVEC	blood vessel
48	chr1:222884400-222887200	Active TSS	NHEK	skin
49	chr1:222884400-222887400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:222884400-222887400	Active TSS	Cortex derived primary cultured neurospheres	brain

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