Variant report

Variant	rs1254961
Chromosome Location	chr10:43698980-43698981
allele	C/G
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	chr10:43698109-43699491	K562	blood:	n/a	n/a
2	POLR2A	chr10:43698951-43699415	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr10:43698941-43699401	ECC-1	luminal epithelium:	n/a	chr10:43699274-43699284
4	MAX	chr10:43697592-43699700	K562	blood:	n/a	chr10:43699657-43699666 chr10:43698135-43698144 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
5	RCOR1	chr10:43697650-43699564	K562	blood:	n/a	n/a
6	ELF1	chr10:43698866-43699404	GM12878	blood:	n/a	n/a
7	MAX	chr10:43698561-43699339	K562	blood:	n/a	chr10:43699274-43699284
8	ZMIZ1	chr10:43698836-43699365	K562	blood:	n/a	n/a
9	IRF1	chr10:43697593-43699654	K562	blood:	n/a	chr10:43698081-43698095
10	MAX	chr10:43697624-43700114	K562	blood:	n/a	chr10:43699657-43699666 chr10:43698135-43698144 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
11	MYC	chr10:43697676-43699784	K562	blood:	n/a	chr10:43699657-43699666 chr10:43698135-43698144 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
12	JUND	chr10:43698924-43699290	K562	blood:	n/a	n/a
13	POLR2A	chr10:43698720-43699419	K562	blood:	n/a	n/a
14	MAX	chr10:43698969-43699845	H1-hESC	embryonic stem cell:	n/a	chr10:43699657-43699666 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
15	TBP	chr10:43698938-43699644	K562	blood:	n/a	n/a
16	TAF1	chr10:43698820-43699434	ECC-1	luminal epithelium:	n/a	n/a
17	SIN3A	chr10:43698690-43699586	H1-hESC	embryonic stem cell:	n/a	chr10:43698958-43698971
18	MAX	chr10:43698856-43699449	ECC-1	luminal epithelium:	n/a	chr10:43699274-43699284
19	TBP	chr10:43698924-43699220	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3AK20	chr10:43698674-43699358	K562	blood:	n/a	n/a
21	CHD2	chr10:43698462-43699300	K562	blood:	n/a	n/a
22	POLR2A	chr10:43698452-43699407	K562	blood:	n/a	n/a
23	RCOR1	chr10:43698766-43699203	K562	blood:	n/a	n/a
24	ZBTB7A	chr10:43698528-43699062	ECC-1	luminal epithelium:	n/a	n/a
25	ZBTB7A	chr10:43697625-43699717	K562	blood:	n/a	chr10:43699426-43699434 chr10:43697980-43697989
26	TBL1XR1	chr10:43698897-43699213	K562	blood:	n/a	n/a
27	MAZ	chr10:43697573-43699701	K562	blood:	n/a	chr10:43699657-43699666 chr10:43698135-43698144 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
28	POLR2A	chr10:43698863-43699332	ECC-1	luminal epithelium:	n/a	n/a
29	BHLHE40	chr10:43698653-43699582	K562	blood:	n/a	chr10:43699310-43699326
30	ZBTB7A	chr10:43697645-43699019	K562	blood:	n/a	chr10:43697980-43697989
31	CCNT2	chr10:43698852-43699271	K562	blood:	n/a	n/a
32	UBTF	chr10:43698777-43699345	K562	blood:	n/a	n/a
33	POLR2A	chr10:43698697-43699408	H1-hESC	embryonic stem cell:	n/a	n/a
34	HMGN3	chr10:43697654-43699668	K562	blood:	n/a	n/a
35	POLR2A	chr10:43698844-43699345	HCT-116	colon:	n/a	n/a
36	MYC	chr10:43697598-43699770	K562	blood:	n/a	chr10:43699657-43699666 chr10:43698135-43698144 chr10:43699657-43699666 chr10:43699500-43699507 chr10:43699657-43699666 chr10:43699274-43699284 chr10:43699657-43699667 chr10:43699655-43699664
37	HEY1	chr10:43698924-43699327	K562	blood:	n/a	n/a
38	E2F6	chr10:43698805-43699781	K562	blood:	n/a	n/a
39	MXI1	chr10:43698952-43699368	K562	blood:	n/a	n/a
40	ZNF384	chr10:43698889-43699025	K562	blood:	n/a	n/a
41	GTF2B	chr10:43698927-43699030	K562	blood:	n/a	n/a
42	POLR2A	chr10:43698610-43699320	K562	blood:	n/a	n/a
43	NR2F2	chr10:43698341-43699567	K562	blood:	n/a	n/a
44	BACH1	chr10:43698778-43699232	H1-hESC	embryonic stem cell:	n/a	n/a
45	SP1	chr10:43698882-43699659	H1-hESC	embryonic stem cell:	n/a	chr10:43699273-43699284
46	POLR2A	chr10:43698890-43699405	HCT-116	colon:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr10:43698931-43698981	AoSMC	blood vessel:	n/a
2	chr10:43698931-43698981	SK-N-MC	brain:	n/a
3	chr10:43698931-43698981	Jurkat	blood:	n/a
4	chr10:43698931-43698981	AG10803	skin:	n/a
5	chr10:43698931-43698981	BJ	skin:	n/a
6	chr10:43698931-43698981	BE2_C	brain:	n/a
7	chr10:43698931-43698981	GM19239	blood:	n/a
8	chr10:43698931-43698981	NHBE	bronchial:	n/a
9	chr10:43698931-43698981	HUVEC	blood vessel:	n/a
10	chr10:43698931-43698981	HL-60	blood:	n/a
11	chr10:43698931-43698981	IMR90	lung:	fetal
12	chr10:43698931-43698981	HEEpiC	esophagus:	n/a
13	chr10:43698931-43698981	K562	blood:	n/a
14	chr10:43698931-43698981	SKMC	muscle:	n/a
15	chr10:43698931-43698981	ECC-1	luminal epithelium:	n/a
16	chr10:43698931-43698981	HRE	kidney:	n/a
17	chr10:43698931-43698981	Hepatocyte	liver:	n/a
18	chr10:43698931-43698981	HepG2	liver:	n/a
19	chr10:43698931-43698981	HAEpiC	amniotic membrane:	n/a
20	chr10:43698931-43698981	AG04450	lung:	fetal
21	chr10:43698931-43698981	MCF10A-Er-Src	breast:	n/a
22	chr10:43698931-43698981	NHDF-neo	bronchial:	n/a
23	chr10:43698931-43698981	AG04449	skin:	fetal
24	chr10:43698931-43698981	GM12891	blood:	n/a
25	chr10:43698931-43698981	U87	brain:	n/a
26	chr10:43698931-43698981	Caco-2	colon:	n/a
27	chr10:43698931-43698981	HCF	heart:	n/a
28	chr10:43698931-43698981	AG09319	gingival:	n/a
29	chr10:43698931-43698981	PrEC	prostate:	n/a
30	chr10:43698931-43698981	NH-A	brain:	n/a
31	chr10:43698931-43698981	HCM	heart:	n/a
32	chr10:43698931-43698981	AG09309	skin:	n/a
33	chr10:43698931-43698981	HIPEpiC	eye:	n/a
34	chr10:43698931-43698981	ProgFib	skin:	n/a
35	chr10:43698931-43698981	HRPEpiC	eye:	n/a
36	chr10:43698931-43698981	HCT-116	colon:	n/a
37	chr10:43698931-43698981	HEK293	kidney:	embryo
38	chr10:43698931-43698981	NB4	blood:	n/a
39	chr10:43698931-43698981	Hela-S3	cervix:	n/a
40	chr10:43698931-43698981	A549	lung:	n/a
41	chr10:43698931-43698981	HCPEpiC	choroid plexus:	n/a
42	chr10:43698931-43698981	H1-hESC	embryonic stem cell:	embryo
43	chr10:43698931-43698981	PFSK-1	brain:	n/a
44	chr10:43698931-43698981	HNPCEpiC	eye:	n/a
45	chr10:43698931-43698981	RPTEC	kidney:	n/a
46	chr10:43698931-43698981	HRCEpiC	kidney:	n/a
47	chr10:43698931-43698981	GM12892	blood:	n/a
48	chr10:43698931-43698981	HMEC	breast:	n/a
49	chr10:43698931-43698981	CMK	blood:	n/a
50	chr10:43698931-43698981	PANC-1	pancreas:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:43698957..43702295-chr10:43702554..43706038,5	K562	blood:
2	chr10:43696369..43700743-chr10:43891529..43894634,3	K562	blood:
3	chr10:43696835..43700131-chr10:43902185..43905182,4	K562	blood:
4	chr10:43696064..43699246-chr10:43901638..43904576,3	K562	blood:
5	chr10:43632409..43636039-chr10:43698014..43700588,4	K562	blood:
6	chr10:43632694..43635237-chr10:43697053..43700182,3	MCF-7	breast:
7	chr10:43632409..43636039-chr10:43698014..43700588,6	K562	blood:
8	chr10:43698632..43700457-chr10:43704012..43705797,2	K562	blood:
9	chr10:43697420..43700683-chr10:43890424..43894292,4	K562	blood:

Variant related genes	Relation type
RASGEF1A	TF binding region
RASGEF1A	CpG island
ENSG00000169813	Chromatin interaction
ENSG00000198915	Chromatin interaction
ENSG00000169826	Chromatin interaction
ENSG00000273008	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10793423	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12358897	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2115818	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2256550	0.83[ASN][1000 genomes]
rs2435341	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2435374	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2435379	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2435380	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2505547	0.81[CHB][hapmap]
rs2505552	0.92[ASN][1000 genomes]
rs2505556	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2565202	0.84[ASN][1000 genomes]
rs2742236	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2914985	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2914986	0.93[ASN][1000 genomes]
rs3004212	0.82[CHB][hapmap]
rs4648314	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7915431	1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs9787519	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534548	chr10:42890664-43729688	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv430159	chr10:43291894-43946294	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv895082	chr10:43530071-43755506	Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv895083	chr10:43549708-43765485	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv916378	chr10:43622151-43868356	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1043661	chr10:43626619-43890162	Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv540574	chr10:43626619-43890162	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	esv1831010	chr10:43674916-43759185	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking 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	4 gene(s)	inside rSNPs	diseases
9	nsv895084	chr10:43688505-43765485	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv466881	chr10:43695049-43799588	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv550696	chr10:43695049-43799588	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv895085	chr10:43695049-43804617	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv3402305	chr10:43697246-43699869	Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:43675600-43700600	Weak transcription	A549	lung
2	chr10:43697200-43699400	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr10:43697400-43699400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr10:43697400-43699400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr10:43697400-43699400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr10:43697600-43699000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr10:43697600-43699000	Active TSS	HUVEC	blood vessel
8	chr10:43697600-43699000	Active TSS	K562	blood
9	chr10:43697600-43699000	Active TSS	NHEK	skin
10	chr10:43697600-43699200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr10:43697600-43699400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr10:43697600-43699400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr10:43697600-43699400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:43697600-43699400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr10:43697600-43699400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr10:43697600-43699400	Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr10:43697600-43699400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr10:43697600-43699400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr10:43697800-43699000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr10:43697800-43699200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:43697800-43699200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:43697800-43699400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr10:43698000-43699000	Active TSS	Fetal Intestine Large	intestine
24	chr10:43698000-43699000	Active TSS	Thymus	Thymus
25	chr10:43698000-43699200	Enhancers	Primary B cells from cord blood	blood
26	chr10:43698000-43699200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr10:43698000-43699200	Active TSS	Colonic Mucosa	Colon
28	chr10:43698000-43699200	Active TSS	Duodenum Mucosa	Duodenum
29	chr10:43698000-43699200	Active TSS	Fetal Intestine Small	intestine
30	chr10:43698000-43699400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr10:43698000-43699400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr10:43698000-43699800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:43698000-43700000	Enhancers	Lung	lung
34	chr10:43698000-43700200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr10:43698000-43700400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr10:43698000-43700400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:43698000-43700600	Weak transcription	Brain Angular Gyrus	brain
38	chr10:43698000-43722800	Weak transcription	Gastric	stomach
39	chr10:43698200-43699200	Bivalent Enhancer	Fetal Stomach	stomach
40	chr10:43698200-43699200	Enhancers	Fetal Thymus	thymus
41	chr10:43698200-43700200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr10:43698200-43700400	Weak transcription	Brain Anterior Caudate	brain
43	chr10:43698200-43700600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr10:43698200-43700600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr10:43698200-43706600	Weak transcription	Brain Hippocampus Middle	brain
46	chr10:43698200-43707400	Weak transcription	Brain Substantia Nigra	brain
47	chr10:43698400-43699000	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr10:43698400-43699000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr10:43698400-43699000	Active TSS	Pancreas	Pancrea
50	chr10:43698400-43699200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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