Variant report

Variant	rs2231331
Chromosome Location	chr13:38924117-38924118
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	ETS1	chr13:38923516-38924167	GM12878	blood:	n/a	chr13:38923618-38923629 chr13:38923689-38923705
2	E2F4	chr13:38922884-38924685	MCF10A-Er-Src	breast:	n/a	chr13:38923618-38923627
3	POLR2A	chr13:38923835-38924667	HL-60	blood:	n/a	n/a
4	USF2	chr13:38923829-38924596	GM12878	blood:	n/a	n/a
5	SIN3A	chr13:38923383-38924452	GM12878	blood:	n/a	n/a
6	PBX3	chr13:38923462-38924169	SK-N-SH	brain:	n/a	n/a
7	MXI1	chr13:38923118-38924602	GM12878	blood:	n/a	chr13:38923581-38923596 chr13:38924465-38924474 chr13:38924482-38924491
8	POLR2A	chr13:38923020-38924796	HepG2	liver:	n/a	n/a
9	POLR2A	chr13:38923272-38924545	NB4	blood:	n/a	n/a
10	POLR2A	chr13:38923835-38924468	GM12891	blood:	n/a	n/a
11	E2F6	chr13:38923917-38924557	K562	blood:	n/a	chr13:38924114-38924125
12	NFIC	chr13:38923232-38924375	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr13:38923359-38926192	K562	blood:	n/a	n/a
14	SP1	chr13:38923460-38924190	GM12878	blood:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
15	POLR2A	chr13:38923438-38924628	K562	blood:	n/a	n/a
16	POLR2A	chr13:38923820-38924537	PFSK-1	brain:	n/a	n/a
17	SP1	chr13:38923476-38924241	HCT-116	colon:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
18	TAF1	chr13:38923761-38924436	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr13:38923770-38924573	GM12891	blood:	n/a	n/a
20	SP1	chr13:38923410-38924242	A549	lung:	n/a	chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923617-38923626 chr13:38923617-38923627 chr13:38923616-38923628 chr13:38923616-38923628 chr13:38923618-38923627
21	CREB1	chr13:38923626-38924164	ECC-1	luminal epithelium:	n/a	n/a
22	MYC	chr13:38923685-38924274	HepG2	liver:	n/a	n/a
23	ARID3A	chr13:38923197-38924647	HepG2	liver:	n/a	chr13:38923245-38923261 chr13:38923246-38923262
24	MXI1	chr13:38923153-38924582	HepG2	liver:	n/a	chr13:38923581-38923596 chr13:38924465-38924474 chr13:38924482-38924491
25	TAF1	chr13:38923858-38924181	HepG2	liver:	n/a	n/a
26	POLR2A	chr13:38923841-38924155	H1-hESC	embryonic stem cell:	n/a	n/a
27	MAZ	chr13:38923369-38924553	GM12878	blood:	n/a	chr13:38923623-38923633
28	POLR2A	chr13:38923419-38924609	ProgFib	skin:	n/a	n/a
29	ATF2	chr13:38923548-38924180	GM12878	blood:	n/a	n/a
30	TCF12	chr13:38923465-38924206	A549	lung:	n/a	chr13:38924064-38924073
31	ATF2	chr13:38923624-38924243	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr13:38923804-38924265	A549	lung:	n/a	n/a
33	POLR2A	chr13:38923738-38924598	GM12878	blood:	n/a	n/a
34	ZNF143	chr13:38923658-38924529	K562	blood:	n/a	n/a
35	POLR2A	chr13:38923197-38924792	K562	blood:	n/a	n/a
36	MYC	chr13:38923768-38924515	MCF-7	breast:	n/a	n/a
37	RUNX3	chr13:38923607-38924237	GM12878	blood:	n/a	n/a
38	GABPA	chr13:38923900-38924131	GM12878	blood:	n/a	n/a
39	POLR2A	chr13:38923441-38924500	H1-neurons	neurons:	n/a	n/a
40	POLR2A	chr13:38923811-38924526	K562	blood:	n/a	n/a
41	TBP	chr13:38923390-38924189	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr13:38923107-38924549	Hela-S3	cervix:	n/a	chr13:38923623-38923633
43	TAF1	chr13:38923810-38924547	ECC-1	luminal epithelium:	n/a	n/a
44	EP300	chr13:38923060-38924513	K562	blood:	n/a	chr13:38923540-38923549 chr13:38924064-38924074
45	MAX	chr13:38923171-38924713	GM12878	blood:	n/a	chr13:38923623-38923633
46	SP4	chr13:38923397-38924205	H1-hESC	embryonic stem cell:	n/a	chr13:38923614-38923630
47	POU2F2	chr13:38923764-38924218	GM12891	blood:	n/a	n/a
48	RCOR1	chr13:38923559-38924552	HepG2	liver:	n/a	n/a
49	ELF1	chr13:38923388-38924284	MCF-7	breast:	n/a	n/a
50	TBP	chr13:38923646-38924564	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:38923439..38924342-chr19:36630421..36631091,2	Hela-S3	cervix:
2	chr13:38921186..38924004-chr13:38924043..38925621,2	MCF-7	breast:
3	chr10:126604859..126605843-chr13:38923544..38924473,3	NB4	blood:
4	chr1:46806181..46806774-chr13:38923650..38924520,2	Hela-S3	cervix:

Variant related genes	Relation type
UFM1	TF binding region
ENSG00000117481	Chromatin interaction
ENSG00000249456	Chromatin interaction
ENSG00000120686	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10514844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1330958	1.00[CEU][hapmap]
rs1330960	1.00[CEU][hapmap]
rs1330964	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1330965	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1330967	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330976	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1501853	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1576610	1.00[CEU][hapmap]
rs17057716	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17057738	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17057757	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17230677	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17231243	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17233628	1.00[ASN][1000 genomes]
rs17296794	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17297214	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17299513	1.00[ASN][1000 genomes]
rs1878948	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980984	1.00[CEU][hapmap]
rs2019520	1.00[CEU][hapmap]
rs2094893	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2104818	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2150469	1.00[CEU][hapmap]
rs2231323	1.00[CEU][hapmap]
rs2231328	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2231330	1.00[CEU][hapmap]
rs2231332	1.00[CEU][hapmap]
rs2323881	1.00[ASN][1000 genomes]
rs2323935	1.00[ASN][1000 genomes]
rs2323936	1.00[ASN][1000 genomes]
rs2323938	1.00[ASN][1000 genomes]
rs2323939	1.00[ASN][1000 genomes]
rs2323940	1.00[ASN][1000 genomes]
rs2481877	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2481879	1.00[CEU][hapmap]
rs2481880	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2485783	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2485785	1.00[CEU][hapmap]
rs2485786	1.00[CEU][hapmap]
rs2496466	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496473	1.00[CEU][hapmap]
rs2496475	1.00[CEU][hapmap]
rs2496476	1.00[CEU][hapmap]
rs4310732	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943583	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4943584	1.00[CEU][hapmap]
rs4943585	1.00[CEU][hapmap]
rs514830	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526103	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546681	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs552296	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55671132	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56329947	1.00[ASN][1000 genomes]
rs58014955	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs605579	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608497	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61087779	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61569024	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652460	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563610	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317565	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73180715	1.00[ASN][1000 genomes]
rs73180716	1.00[ASN][1000 genomes]
rs73180718	1.00[ASN][1000 genomes]
rs73180719	1.00[ASN][1000 genomes]
rs73180721	1.00[ASN][1000 genomes]
rs73180722	1.00[ASN][1000 genomes]
rs73180723	1.00[ASN][1000 genomes]
rs73180725	1.00[ASN][1000 genomes]
rs73180728	1.00[ASN][1000 genomes]
rs73180729	1.00[ASN][1000 genomes]
rs73180730	1.00[ASN][1000 genomes]
rs73180731	1.00[ASN][1000 genomes]
rs73180736	1.00[ASN][1000 genomes]
rs73180738	1.00[ASN][1000 genomes]
rs73180740	1.00[ASN][1000 genomes]
rs7334232	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73460206	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73460223	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73460238	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73460239	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73460244	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73462348	1.00[ASN][1000 genomes]
rs73464368	1.00[ASN][1000 genomes]
rs73464376	1.00[ASN][1000 genomes]
rs74047533	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	1.00[CEU][hapmap]
rs9532209	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9548318	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9548386	1.00[ASN][1000 genomes]
rs9594267	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv561512	chr13:38881318-38930893	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv900005	chr13:38881318-38932949	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 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	chr13:38922400-38925200	Active TSS	Breast Myoepithelial Primary Cells	Breast
2	chr13:38922600-38924800	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr13:38922600-38925000	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr13:38922600-38925000	Active TSS	K562	blood
5	chr13:38922600-38925200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr13:38922600-38925200	Active TSS	HSMMtube	muscle
7	chr13:38922600-38926000	Active TSS	Right Atrium	heart
8	chr13:38922800-38924200	Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr13:38922800-38924400	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr13:38922800-38924400	Active TSS	Thymus	Thymus
11	chr13:38922800-38924600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:38922800-38924600	Active TSS	Brain Cingulate Gyrus	brain
13	chr13:38922800-38924600	Active TSS	Brain Germinal Matrix	brain
14	chr13:38922800-38924600	Active TSS	Brain Substantia Nigra	brain
15	chr13:38922800-38924600	Active TSS	Rectal Smooth Muscle	rectum
16	chr13:38922800-38924600	Active TSS	Stomach Smooth Muscle	stomach
17	chr13:38922800-38924800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr13:38922800-38924800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:38922800-38924800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:38922800-38924800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr13:38922800-38924800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr13:38922800-38924800	Active TSS	Fetal Kidney	kidney
23	chr13:38922800-38924800	Active TSS	Fetal Stomach	stomach
24	chr13:38922800-38925000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr13:38922800-38925000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr13:38922800-38925000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:38922800-38925000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:38922800-38925000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:38922800-38925000	Active TSS	Aorta	Aorta
30	chr13:38922800-38925000	Active TSS	Fetal Intestine Large	intestine
31	chr13:38922800-38925000	Active TSS	GM12878-XiMat	blood
32	chr13:38922800-38925200	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr13:38922800-38925200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:38922800-38925200	Active TSS	NHLF	lung
35	chr13:38922800-38926200	Active TSS	Right Ventricle	heart
36	chr13:38923000-38924400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr13:38923000-38924400	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr13:38923000-38924600	Active TSS	Brain Anterior Caudate	brain
39	chr13:38923000-38924600	Active TSS	Colon Smooth Muscle	Colon
40	chr13:38923000-38924600	Active TSS	Fetal Heart	heart
41	chr13:38923000-38924800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr13:38923000-38924800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr13:38923000-38924800	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr13:38923000-38924800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr13:38923000-38924800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr13:38923000-38924800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr13:38923000-38924800	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr13:38923000-38924800	Active TSS	Esophagus	oesophagus
49	chr13:38923000-38924800	Active TSS	Sigmoid Colon	Sigmoid Colon
50	chr13:38923000-38924800	Active TSS	Small Intestine	intestine

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