Variant report

Variant	rs2031775
Chromosome Location	chr13:48611543-48611544
allele	C/T
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	PBX3	chr13:48611414-48613130	SK-N-SH	brain:	n/a	n/a
2	CUX1	chr13:48611447-48612612	K562	blood:	n/a	n/a
3	MAFK	chr13:48611469-48612374	IMR90	lung:	n/a	n/a
4	POLR2A	chr13:48611354-48612489	K562	blood:	n/a	n/a
5	MYC	chr13:48611502-48612383	MCF10A-Er-Src	breast:	n/a	n/a
6	YY1	chr13:48611372-48612044	H1-hESC	embryonic stem cell:	n/a	chr13:48611812-48611826 chr13:48611786-48611795
7	POLR2A	chr13:48611355-48612536	HCT-116	colon:	n/a	n/a
8	RAD21	chr13:48611403-48612410	IMR90	lung:	n/a	chr13:48612206-48612220 chr13:48612205-48612224
9	RELA	chr13:48611217-48612718	GM18951	blood:	n/a	n/a
10	POLR2A	chr13:48611415-48612541	PBDE	blood:	n/a	n/a
11	SP1	chr13:48611202-48612408	H1-hESC	embryonic stem cell:	n/a	chr13:48611787-48611798
12	MAX	chr13:48611396-48612442	SK-N-SH	brain:	n/a	n/a
13	SIN3AK20	chr13:48611526-48612242	A549	lung:	n/a	n/a
14	BCL3	chr13:48611376-48612364	A549	lung:	n/a	chr13:48611740-48611749 chr13:48611818-48611831 chr13:48611812-48611825 chr13:48611845-48611854 chr13:48612215-48612223
15	NFATC1	chr13:48611525-48612570	GM12878	blood:	n/a	n/a
16	REST	chr13:48611307-48612509	HL-60	blood:	n/a	chr13:48611738-48611751 chr13:48611734-48611754 chr13:48611492-48611505 chr13:48611740-48611749 chr13:48611738-48611751
17	MXI1	chr13:48611334-48612424	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr13:48611409-48612415	H1-hESC	embryonic stem cell:	n/a	chr13:48612206-48612220 chr13:48612205-48612224
19	POLR2A	chr13:48611457-48612488	GM10847	blood:	n/a	n/a
20	POLR2A	chr13:48611341-48612559	HUVEC	blood vessel:	n/a	n/a
21	SIN3AK20	chr13:48611420-48612468	SK-N-SH	brain:	n/a	n/a
22	E2F6	chr13:48611481-48612310	A549	lung:	n/a	n/a
23	POLR2A	chr13:48611427-48612179	U87	brain:	n/a	n/a
24	TBP	chr13:48611451-48612438	GM12878	blood:	n/a	n/a
25	CHD1	chr13:48611490-48612444	GM12878	blood:	n/a	n/a
26	MXI1	chr13:48611298-48612377	K562	blood:	n/a	n/a
27	POU2F2	chr13:48611320-48612573	GM12878	blood:	n/a	chr13:48611620-48611633 chr13:48611563-48611585 chr13:48611620-48611633 chr13:48611618-48611632 chr13:48611621-48611635 chr13:48611385-48611406 chr13:48611620-48611633
28	POLR2A	chr13:48611391-48612585	GM12878	blood:	n/a	n/a
29	POLR2A	chr13:48611393-48612569	H1-neurons	neurons:	n/a	n/a
30	MYC	chr13:48611482-48612515	K562	blood:	n/a	n/a
31	BRCA1	chr13:48611542-48612276	HepG2	liver:	n/a	n/a
32	SP1	chr13:48611399-48612474	GM12878	blood:	n/a	chr13:48611787-48611798
33	POLR2A	chr13:48611324-48612611	GM19193	blood:	n/a	n/a
34	MAX	chr13:48611453-48612461	GM12878	blood:	n/a	n/a
35	SIN3A	chr13:48611335-48612403	GM12878	blood:	n/a	chr13:48611741-48611754 chr13:48612216-48612229
36	TAF1	chr13:48611472-48612352	Hela-S3	cervix:	n/a	n/a
37	ZNF263	chr13:48611390-48612452	HEK293-T-REx	kidney:	n/a	n/a
38	MXI1	chr13:48611391-48613186	GM12878	blood:	n/a	n/a
39	ELF1	chr13:48611463-48612497	HCT-116	colon:	n/a	chr13:48611786-48611795 chr13:48611813-48611825
40	HDAC2	chr13:48611383-48611949	K562	blood:	n/a	n/a
41	ZNF143	chr13:48611464-48612422	H1-hESC	embryonic stem cell:	n/a	chr13:48612181-48612199
42	POLR2A	chr13:48611092-48612781	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr13:48611457-48612299	U87	brain:	n/a	n/a
44	YY1	chr13:48611518-48612465	HepG2	liver:	n/a	chr13:48611812-48611826 chr13:48611786-48611795
45	POLR2A	chr13:48611320-48612661	GM18951	blood:	n/a	n/a
46	JUND	chr13:48611303-48612444	H1-hESC	embryonic stem cell:	n/a	n/a
47	SIN3AK20	chr13:48611525-48611929	PANC-1	pancreas:	n/a	n/a
48	POLR2A	chr13:48611330-48612493	GM15510	blood:	n/a	n/a
49	POLR2A	chr13:48611178-48612552	MCF10A-Er-Src	breast:	n/a	n/a
50	ELF1	chr13:48611427-48612357	GM12878	blood:	n/a	chr13:48611786-48611795 chr13:48611813-48611825

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr13:48611517-48611567	GM12892	blood:	n/a
2	chr13:48611517-48611567	U87	brain:	n/a
3	chr13:48611517-48611567	AG04449	skin:	fetal
4	chr13:48611517-48611567	RPTEC	kidney:	n/a
5	chr13:48611517-48611567	SKMC	muscle:	n/a
6	chr13:48611517-48611567	SK-N-SH	brain:	n/a
7	chr13:48611517-48611567	IMR90	lung:	fetal
8	chr13:48611517-48611567	HRE	kidney:	n/a
9	chr13:48611517-48611567	NB4	blood:	n/a
10	chr13:48611517-48611567	HRPEpiC	eye:	n/a
11	chr13:48611517-48611567	AG10803	skin:	n/a
12	chr13:48611517-48611567	HCM	heart:	n/a
13	chr13:48611517-48611567	LNCaP	prostate:	n/a
14	chr13:48611517-48611567	ProgFib	skin:	n/a
15	chr13:48611517-48611567	SK-N-SH_RA	brain:	n/a
16	chr13:48611517-48611567	CMK	blood:	n/a
17	chr13:48611517-48611567	H1-hESC	embryonic stem cell:	embryo
18	chr13:48611517-48611567	SK-N-MC	brain:	n/a
19	chr13:48611517-48611567	ECC-1	luminal epithelium:	n/a
20	chr13:48611517-48611567	MCF10A-Er-Src	breast:	n/a
21	chr13:48611517-48611567	AG04450	lung:	fetal
22	chr13:48611517-48611567	T-47D	breast:	n/a
23	chr13:48611517-48611567	HepG2	liver:	n/a
24	chr13:48611517-48611567	BJ	skin:	n/a
25	chr13:48611517-48611567	NHBE	bronchial:	n/a
26	chr13:48611517-48611567	NH-A	brain:	n/a
27	chr13:48611517-48611567	AoSMC	blood vessel:	n/a
28	chr13:48611517-48611567	AG09319	gingival:	n/a
29	chr13:48611517-48611567	Hepatocyte	liver:	n/a
30	chr13:48611517-48611567	HNPCEpiC	eye:	n/a
31	chr13:48611517-48611567	MCF-7	breast:	n/a
32	chr13:48611517-48611567	Caco-2	colon:	n/a
33	chr13:48611517-48611567	HPAEpiC	pulmonary alveolar:	n/a
34	chr13:48611517-48611567	HMEC	breast:	n/a
35	chr13:48611517-48611567	BE2_C	brain:	n/a
36	chr13:48611517-48611567	PrEC	prostate:	n/a
37	chr13:48611517-48611567	PFSK-1	brain:	n/a
38	chr13:48611517-48611567	GM06990	blood:	n/a
39	chr13:48611517-48611567	K562	blood:	n/a
40	chr13:48611517-48611567	HCT-116	colon:	n/a
41	chr13:48611517-48611567	SAEC	small airway:	n/a
42	chr13:48611517-48611567	HUVEC	blood vessel:	n/a
43	chr13:48611517-48611567	HCF	heart:	n/a
44	chr13:48611517-48611567	HCPEpiC	choroid plexus:	n/a
45	chr13:48611517-48611567	Hela-S3	cervix:	n/a
46	chr13:48611517-48611567	HL-60	blood:	n/a
47	chr13:48611517-48611567	GM12891	blood:	n/a
48	chr13:48611517-48611567	NHDF-neo	bronchial:	n/a
49	chr13:48611517-48611567	PANC-1	pancreas:	n/a
50	chr13:48611517-48611567	Jurkat	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:48573666..48577274-chr13:48610467..48613685,4	MCF-7	breast:
2	chr13:48610643..48613395-chr13:48668732..48670612,2	MCF-7	breast:
3	chr13:48611090..48611973-chr14:100704137..100705031,2	Hela-S3	cervix:
4	chr13:30424219..30424825-chr13:48611138..48612130,2	NB4	blood:

Variant related genes	Relation type
NUDT15	TF binding region
NUDT15	CpG island
ENSG00000136146	Chromatin interaction
ENSG00000100811	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000258982	Chromatin interaction
ENSG00000122042	Chromatin interaction
ENSG00000136143	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2406701	0.81[EUR][1000 genomes]
rs28794608	0.81[EUR][1000 genomes]
rs4496017	0.83[EUR][1000 genomes]
rs55845516	0.83[EUR][1000 genomes]
rs6561423	1.00[GIH][hapmap];0.83[EUR][1000 genomes]
rs7317676	0.84[EUR][1000 genomes]
rs7318370	0.86[EUR][1000 genomes]
rs7319779	0.81[EUR][1000 genomes]
rs7325292	0.87[EUR][1000 genomes]
rs7983350	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs840431	0.83[EUR][1000 genomes]
rs840434	1.00[GIH][hapmap]
rs9316341	0.83[EUR][1000 genomes]
rs9591121	1.00[GIH][hapmap]
rs9591125	0.81[EUR][1000 genomes]
rs9591126	0.83[EUR][1000 genomes]
rs9591128	0.83[EUR][1000 genomes]
rs9595826	0.83[EUR][1000 genomes]
rs9595827	0.83[EUR][1000 genomes]
rs9595828	0.83[EUR][1000 genomes]
rs9595830	0.83[EUR][1000 genomes]
rs9595831	0.83[EUR][1000 genomes]
rs9595832	0.84[EUR][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	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 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	chr13:48610400-48611600	Flanking Active TSS	Dnd41	blood
2	chr13:48610400-48612800	Active TSS	K562	blood
3	chr13:48610400-48613000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr13:48610400-48613200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:48610600-48611600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:48610600-48611600	Flanking Active TSS	GM12878-XiMat	blood
7	chr13:48610800-48611600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr13:48610800-48611600	Flanking Active TSS	Fetal Lung	lung
9	chr13:48610800-48611600	Flanking Active TSS	NHEK	skin
10	chr13:48610800-48611800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr13:48610800-48612400	Active TSS	H1 Cell Line	embryonic stem cell
12	chr13:48610800-48612800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr13:48610800-48613000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:48610800-48613000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr13:48610800-48613200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr13:48611000-48611600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr13:48611000-48611600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr13:48611000-48611600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr13:48611000-48611600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:48611000-48611600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr13:48611000-48611600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:48611000-48611600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr13:48611000-48611600	Flanking Active TSS	Fetal Kidney	kidney
24	chr13:48611000-48611600	Flanking Active TSS	Thymus	Thymus
25	chr13:48611000-48611600	Flanking Active TSS	HSMM	muscle
26	chr13:48611000-48611600	Flanking Active TSS	NHLF	lung
27	chr13:48611000-48611800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr13:48611000-48611800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:48611000-48611800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr13:48611000-48611800	Flanking Active TSS	HUVEC	blood vessel
31	chr13:48611000-48612600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:48611000-48612600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr13:48611000-48612800	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr13:48611000-48612800	Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:48611000-48613000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:48611000-48613000	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr13:48611000-48613000	Active TSS	A549	lung
38	chr13:48611000-48613400	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr13:48611200-48611600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr13:48611200-48611600	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr13:48611200-48611600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:48611200-48611600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr13:48611200-48611600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr13:48611200-48611600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:48611200-48611600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr13:48611200-48611600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
47	chr13:48611200-48611600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr13:48611200-48611600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr13:48611200-48611600	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr13:48611200-48611600	Flanking Active TSS	Brain Cingulate Gyrus	brain

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