Variant report

Variant	rs13423628
Chromosome Location	chr2:97001325-97001326
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	JUND	chr2:97001217-97001995	A549	lung:	n/a	chr2:97001782-97001791
2	POLR2A	chr2:97001063-97002493	K562	blood:	n/a	n/a
3	USF2	chr2:97001325-97001631	H1-hESC	embryonic stem cell:	n/a	chr2:97001466-97001482
4	BRCA1	chr2:97001309-97001705	HepG2	liver:	n/a	n/a
5	E2F1	chr2:97001321-97002021	Hela-S3	cervix:	n/a	chr2:97001458-97001467 chr2:97001780-97001789 chr2:97001608-97001620 chr2:97001603-97001612
6	PML	chr2:97001190-97001599	GM12878	blood:	n/a	n/a
7	RCOR1	chr2:97001271-97002296	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr2:97001113-97002111	SK-N-SH	brain:	n/a	n/a
9	BRCA1	chr2:97001242-97002057	Hela-S3	cervix:	n/a	n/a
10	CEBPD	chr2:97001143-97002054	HepG2	liver:	n/a	n/a
11	PML	chr2:97001124-97002270	K562	blood:	n/a	chr2:97001898-97001906
12	MAX	chr2:97001264-97002010	HepG2	liver:	n/a	n/a
13	POLR2A	chr2:97000890-97002286	PFSK-1	brain:	n/a	n/a
14	MBD4	chr2:97001111-97002519	HepG2	liver:	n/a	n/a
15	SIN3AK20	chr2:97001252-97002044	SK-N-SH	brain:	n/a	n/a
16	E2F6	chr2:97001168-97002155	A549	lung:	n/a	chr2:97001458-97001467 chr2:97001780-97001789 chr2:97001608-97001620 chr2:97001603-97001612
17	NFIC	chr2:97001099-97001888	GM12878	blood:	n/a	n/a
18	YY1	chr2:97001203-97001744	GM12878	blood:	n/a	chr2:97001468-97001482 chr2:97001475-97001489 chr2:97001431-97001445
19	USF2	chr2:97001301-97001954	GM12878	blood:	n/a	chr2:97001466-97001482
20	TAF1	chr2:97001197-97002162	ECC-1	luminal epithelium:	n/a	n/a
21	E2F6	chr2:97001288-97002388	K562	blood:	n/a	chr2:97001458-97001467 chr2:97001780-97001789 chr2:97001608-97001620 chr2:97001603-97001612
22	ZBTB7A	chr2:97001114-97001724	K562	blood:	n/a	n/a
23	POLR2A	chr2:97001131-97002135	GM12878	blood:	n/a	n/a
24	IRF1	chr2:97001292-97002016	K562	blood:	n/a	chr2:97001841-97001850 chr2:97001780-97001789
25	TBP	chr2:97001179-97002169	GM12878	blood:	n/a	n/a
26	USF1	chr2:97001274-97001633	A549	lung:	n/a	chr2:97001466-97001482
27	EGR1	chr2:97001284-97001720	GM12878	blood:	n/a	chr2:97001458-97001467
28	MAX	chr2:97001134-97002468	K562	blood:	n/a	n/a
29	POLR2A	chr2:97001167-97001715	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr2:97001160-97002013	H1-neurons	neurons:	n/a	n/a
31	TAF1	chr2:97001260-97002005	HepG2	liver:	n/a	n/a
32	TCF12	chr2:97001283-97002173	ECC-1	luminal epithelium:	n/a	n/a
33	ZNF143	chr2:97001316-97002072	K562	blood:	n/a	chr2:97001853-97001863
34	MYC	chr2:97001219-97002363	K562	blood:	n/a	n/a
35	CREB1	chr2:97001265-97001647	A549	lung:	n/a	n/a
36	YY1	chr2:97001306-97002007	GM12892	blood:	n/a	chr2:97001812-97001826 chr2:97001468-97001482 chr2:97001475-97001489 chr2:97001431-97001445
37	RFX5	chr2:97001279-97001935	HepG2	liver:	n/a	chr2:97001781-97001790
38	BHLHE40	chr2:97001243-97002042	GM12878	blood:	n/a	chr2:97001466-97001482
39	ZBTB7A	chr2:97001207-97001945	K562	blood:	n/a	n/a
40	CREB1	chr2:97001312-97001815	ECC-1	luminal epithelium:	n/a	n/a
41	MAX	chr2:97001189-97002076	SK-N-SH	brain:	n/a	n/a
42	FOXM1	chr2:97001053-97002247	SK-N-SH	brain:	n/a	n/a
43	GTF3C2	chr2:97000744-97001477	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr2:97001123-97002286	Hela-S3	cervix:	n/a	n/a
45	TEAD4	chr2:97001119-97002431	K562	blood:	n/a	n/a
46	ZNF143	chr2:97001214-97001900	GM12878	blood:	n/a	chr2:97001853-97001863
47	SP1	chr2:97001259-97002008	GM12878	blood:	n/a	chr2:97001668-97001677 chr2:97001736-97001745 chr2:97001779-97001800
48	MXI1	chr2:97001241-97002362	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:97001078-97001702	GM12891	blood:	n/a	n/a
50	POLR2A	chr2:97001144-97002396	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:97001304-97001354	NT2-D1	testis:	n/a
2	chr2:97001301-97001351	PrEC	prostate:	n/a
3	chr2:97001304-97001354	AG09319	gingival:	n/a
4	chr2:97001304-97001354	GM12891	blood:	n/a
5	chr2:97001301-97001351	NT2-D1	testis:	n/a
6	chr2:97001304-97001354	BJ	skin:	n/a
7	chr2:97001281-97001331	HAEpiC	amniotic membrane:	n/a
8	chr2:97001304-97001354	ovcar-3	ovarian:	n/a
9	chr2:97001301-97001351	HEK293	kidney:	embryo
10	chr2:97001281-97001331	MCF-7	breast:	n/a
11	chr2:97001301-97001351	IMR90	lung:	fetal
12	chr2:97001301-97001351	HRCEpiC	kidney:	n/a
13	chr2:97001301-97001351	AoSMC	blood vessel:	n/a
14	chr2:97001301-97001351	PFSK-1	brain:	n/a
15	chr2:97001304-97001354	HEK293	kidney:	embryo
16	chr2:97001281-97001331	ECC-1	luminal epithelium:	n/a
17	chr2:97001301-97001351	HCM	heart:	n/a
18	chr2:97001301-97001351	HepG2	liver:	n/a
19	chr2:97001281-97001331	SK-N-MC	brain:	n/a
20	chr2:97001301-97001351	MCF10A-Er-Src	breast:	n/a
21	chr2:97001281-97001331	SK-N-SH_RA	brain:	n/a
22	chr2:97001281-97001331	BJ	skin:	n/a
23	chr2:97001304-97001354	SK-N-SH	brain:	n/a
24	chr2:97001281-97001331	Hela-S3	cervix:	n/a
25	chr2:97001301-97001351	HCPEpiC	choroid plexus:	n/a
26	chr2:97001304-97001354	HAEpiC	amniotic membrane:	n/a
27	chr2:97001301-97001351	SAEC	small airway:	n/a
28	chr2:97001304-97001354	HRE	kidney:	n/a
29	chr2:97001281-97001331	NHDF-neo	bronchial:	n/a
30	chr2:97001281-97001331	HNPCEpiC	eye:	n/a
31	chr2:97001281-97001331	U87	brain:	n/a
32	chr2:97001304-97001354	GM12892	blood:	n/a
33	chr2:97001304-97001354	IMR90	lung:	fetal
34	chr2:97001281-97001331	HEK293	kidney:	embryo
35	chr2:97001304-97001354	AG04449	skin:	fetal
36	chr2:97001301-97001351	SKMC	muscle:	n/a
37	chr2:97001304-97001354	RPTEC	kidney:	n/a
38	chr2:97001281-97001331	MCF10A-Er-Src	breast:	n/a
39	chr2:97001281-97001331	ovcar-3	ovarian:	n/a
40	chr2:97001281-97001331	GM12892	blood:	n/a
41	chr2:97001304-97001354	HRCEpiC	kidney:	n/a
42	chr2:97001281-97001331	HCM	heart:	n/a
43	chr2:97001304-97001354	NH-A	brain:	n/a
44	chr2:97001304-97001354	AG04450	lung:	fetal
45	chr2:97001304-97001354	HUVEC	blood vessel:	n/a
46	chr2:97001301-97001351	Hela-S3	cervix:	n/a
47	chr2:97001281-97001331	T-47D	breast:	n/a
48	chr2:97001301-97001351	NH-A	brain:	n/a
49	chr2:97001301-97001351	HCF	heart:	n/a
50	chr2:97001301-97001351	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96930374..96934423-chr2:97000506..97002803,4	MCF-7	breast:
2	chr2:96929963..96932171-chr2:96999935..97002452,2	K562	blood:
3	chr2:96929992..96934856-chr2:96999935..97004454,8	K562	blood:
4	chr15:76603148..76604121-chr2:97001077..97001691,2	Hela-S3	cervix:
5	chr2:96968671..96973165-chr2:96996066..97004511,14	MCF-7	breast:
6	chr2:96954952..96956896-chr2:96999243..97002059,2	MCF-7	breast:
7	chr2:96969192..96974477-chr2:96999948..97003661,14	K562	blood:
8	chr2:96872884..96875870-chr2:96999913..97003204,4	MCF-7	breast:
9	chr2:96925642..96927214-chr2:97001032..97003514,2	K562	blood:
10	chr2:96970144..96972526-chr2:96999842..97002907,4	MCF-7	breast:

Variant related genes	Relation type
NCAPH	TF binding region
NCAPH	CpG island
ENSG00000144028	Chromatin interaction
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000140374	Chromatin interaction
ENSG00000135956	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs12623853	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS 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	25 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97000400-97002000	Active TSS	Colonic Mucosa	Colon
2	chr2:97000400-97002200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:97000400-97002200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr2:97000400-97002200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:97000400-97002400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:97000400-97002400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:97000400-97002600	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:97000400-97002600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:97000600-97001400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr2:97000600-97001400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr2:97000600-97001800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr2:97000600-97001800	Active TSS	Placenta	Placenta
13	chr2:97000600-97001800	Active TSS	Rectal Smooth Muscle	rectum
14	chr2:97000600-97002000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:97000600-97002000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:97000600-97002000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:97000600-97002000	Active TSS	Brain Angular Gyrus	brain
18	chr2:97000600-97002000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:97000600-97002000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr2:97000600-97002000	Active TSS	Fetal Lung	lung
21	chr2:97000600-97002200	Active TSS	H1 Cell Line	embryonic stem cell
22	chr2:97000600-97002200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:97000600-97002200	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:97000600-97002200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:97000600-97002200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:97000600-97002200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:97000600-97002200	Active TSS	Right Ventricle	heart
28	chr2:97000600-97002200	Active TSS	NHDF-Ad	bronchial
29	chr2:97000600-97002400	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr2:97000600-97002400	Active TSS	HSMMtube	muscle
31	chr2:97000600-97002600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr2:97000600-97002800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:97000800-97001400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:97000800-97001800	Active TSS	Brain Hippocampus Middle	brain
35	chr2:97000800-97001800	Active TSS	Fetal Stomach	stomach
36	chr2:97000800-97001800	Active TSS	Lung	lung
37	chr2:97000800-97001800	Active TSS	Spleen	Spleen
38	chr2:97000800-97001800	Active TSS	HSMM	muscle
39	chr2:97000800-97002000	Active TSS	Primary T cells from cord blood	blood
40	chr2:97000800-97002000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:97000800-97002000	Active TSS	Brain Cingulate Gyrus	brain
42	chr2:97000800-97002000	Active TSS	Brain Substantia Nigra	brain
43	chr2:97000800-97002000	Active TSS	Fetal Intestine Large	intestine
44	chr2:97000800-97002000	Active TSS	Fetal Kidney	kidney
45	chr2:97000800-97002000	Active TSS	Ovary	ovary
46	chr2:97000800-97002000	Active TSS	Psoas Muscle	Psoas
47	chr2:97000800-97002000	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr2:97000800-97002000	Active TSS	Stomach Mucosa	stomach
49	chr2:97000800-97002000	Active TSS	Hela-S3	cervix
50	chr2:97000800-97002000	Active TSS	K562	blood

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