Variant report

Variant	rs8248
Chromosome Location	chr13:49549571-49549572
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	GTF2F1	chr13:49549306-49549827	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr13:49549088-49551311	MCF-7	breast:	n/a	n/a
3	CTCF	chr13:49549560-49549710	NHEK	skin:	n/a	n/a
4	POLR2A	chr13:49548174-49551824	IMR90	lung:	n/a	n/a
5	ZNF143	chr13:49549236-49550640	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr13:49549266-49551238	GM18505	blood:	n/a	n/a
7	REST	chr13:49549074-49551813	H1-neurons	neurons:	n/a	chr13:49550513-49550526 chr13:49550773-49550783 chr13:49549286-49549295
8	TBL1XR1	chr13:49549344-49549942	K562	blood:	n/a	n/a
9	MAX	chr13:49549274-49551205	K562	blood:	n/a	chr13:49549900-49549909
10	POLR2A	chr13:49549457-49551023	GM12878	blood:	n/a	n/a
11	MAX	chr13:49549207-49551236	SK-N-SH	brain:	n/a	chr13:49549900-49549909
12	POLR2A	chr13:49549556-49551187	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr13:49549318-49551233	GM18951	blood:	n/a	n/a
14	MAX	chr13:49549490-49551302	ECC-1	luminal epithelium:	n/a	chr13:49549900-49549909
15	CTCF	chr13:49549560-49549710	AG04450	lung:	n/a	n/a
16	POLR2A	chr13:49549553-49550706	Hela-S3	cervix:	n/a	n/a
17	MAX	chr13:49549219-49551230	HepG2	liver:	n/a	chr13:49549900-49549909
18	TBP	chr13:49549288-49551154	K562	blood:	n/a	n/a
19	ZEB1	chr13:49549568-49551268	HepG2	liver:	n/a	n/a
20	NRF1	chr13:49549427-49551102	SK-N-SH	brain:	n/a	n/a
21	MYC	chr13:49549354-49550500	MCF10A-Er-Src	breast:	n/a	chr13:49549900-49549909
22	CHD2	chr13:49549296-49551023	GM12878	blood:	n/a	n/a
23	MXI1	chr13:49549315-49551704	GM12878	blood:	n/a	n/a
24	EP300	chr13:49549348-49550678	GM12878	blood:	n/a	chr13:49550072-49550081
25	MAX	chr13:49549208-49551133	K562	blood:	n/a	chr13:49549900-49549909
26	JUND	chr13:49549354-49551192	K562	blood:	n/a	n/a
27	POLR2A	chr13:49549539-49551080	MCF-7	breast:	n/a	n/a
28	POLR2A	chr13:49549548-49551070	K562	blood:	n/a	n/a
29	E2F4	chr13:49549408-49549683	MCF10A-Er-Src	breast:	n/a	n/a
30	EGR1	chr13:49549547-49551151	HCT-116	colon:	n/a	chr13:49550677-49550690 chr13:49550649-49550662 chr13:49550675-49550685
31	RAD21	chr13:49549320-49551814	IMR90	lung:	n/a	chr13:49549817-49549831
32	POLR2A	chr13:49549524-49550686	PANC-1	pancreas:	n/a	n/a
33	MYC	chr13:49549360-49551414	K562	blood:	n/a	chr13:49549900-49549909
34	POLR2A	chr13:49549291-49551217	GM19099	blood:	n/a	n/a
35	MAX	chr13:49549290-49551263	GM12878	blood:	n/a	chr13:49549900-49549909
36	MAX	chr13:49549212-49551232	SK-N-SH	brain:	n/a	chr13:49549900-49549909
37	POLR2A	chr13:49549544-49550934	HUVEC	blood vessel:	n/a	n/a
38	POLR2A	chr13:49549527-49551014	K562	blood:	n/a	n/a
39	POLR2A	chr13:49549383-49551330	GM12892	blood:	n/a	n/a
40	RAD21	chr13:49549523-49549852	SK-N-SH_RA	brain:	n/a	chr13:49549817-49549831
41	YY1	chr13:49549285-49550831	SK-N-SH	brain:	n/a	chr13:49550780-49550794 chr13:49550803-49550814 chr13:49550070-49550079 chr13:49550149-49550158 chr13:49550053-49550075 chr13:49550073-49550082 chr13:49550071-49550082
42	GTF2B	chr13:49549398-49549987	K562	blood:	n/a	n/a
43	ELF1	chr13:49549201-49550721	GM12878	blood:	n/a	chr13:49550073-49550082 chr13:49550149-49550158 chr13:49550070-49550079 chr13:49550144-49550156 chr13:49549844-49549853
44	POLR2A	chr13:49549210-49551473	PBDE	blood:	n/a	n/a
45	MXI1	chr13:49549271-49551392	HepG2	liver:	n/a	n/a
46	POLR2A	chr13:49549333-49551059	K562	blood:	n/a	n/a
47	POLR2A	chr13:49549125-49551112	SK-N-MC	brain:	n/a	n/a
48	MAX	chr13:49549558-49550504	A549	lung:	n/a	chr13:49549900-49549909
49	RELA	chr13:49549415-49551177	GM19099	blood:	n/a	n/a
50	WRNIP1	chr13:49549317-49549826	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:49344498..49346343-chr13:49548446..49550486,2	MCF-7	breast:
2	chr13:49549492..49550320-chr15:73075454..73076164,2	NB4	blood:
3	chr10:81106936..81108869-chr13:49549506..49551759,2	MCF-7	breast:
4	chr13:49549495..49551590-chr13:49668953..49673259,5	MCF-7	breast:
5	chr13:49548036..49549716-chr13:49570249..49572622,2	K562	blood:
6	chr13:49549219..49550138-chr16:75669158..75670004,2	NB4	blood:
7	chr13:49511991..49514025-chr13:49547058..49549833,2	K562	blood:
8	chr13:49547950..49551813-chr13:49821954..49825536,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAB39L-4	chr13:49546319-49550047	NONHSAT033727

Variant related genes	Relation type
FNDC3A	TF binding region
ENSG00000159322	Chromatin interaction
ENSG00000225131	Chromatin interaction
ENSG00000065427	Chromatin interaction
ENSG00000102543	Chromatin interaction
ENSG00000108179	Chromatin interaction
ENSG00000199788	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1359066	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1407827	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs1407829	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs1937180	0.83[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs1983805	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2026029	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2146748	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2149498	0.83[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2181539	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2407265	0.84[ASN][1000 genomes]
rs2897633	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4142065	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4258502	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4530025	0.81[JPT][hapmap]
rs4942795	0.82[ASN][1000 genomes]
rs4942796	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs4942799	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs4942800	0.81[JPT][hapmap]
rs6561491	0.87[ASN][1000 genomes]
rs6561496	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs6561497	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs6561504	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs728075	0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7322842	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7329291	0.84[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7333097	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7338529	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[YRI][hapmap]
rs7983885	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7986624	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs7987258	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7988168	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7989175	0.88[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[AMR][1000 genomes]
rs7994368	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7994910	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7995616	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7997118	0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7999513	0.83[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs9316426	0.83[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs9316427	0.84[ASN][1000 genomes]
rs9316428	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9316429	0.89[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes]
rs9526517	0.90[ASN][1000 genomes]
rs9526518	0.82[JPT][hapmap]
rs9526520	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9535136	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9535146	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9535147	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs9535149	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9535156	0.84[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap]
rs9562866	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9568143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568150	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs9568151	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs9568154	0.82[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1792084	chr13:49536705-49549571	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49548400-49551200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr13:49548400-49552200	Active TSS	Aorta	Aorta
3	chr13:49548600-49549600	Flanking Active TSS	Dnd41	blood
4	chr13:49548600-49550000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr13:49548600-49551600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr13:49548800-49549600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
7	chr13:49548800-49549600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:49548800-49549800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:49548800-49549800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr13:49548800-49550000	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr13:49548800-49551600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:49548800-49551600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:49548800-49551600	Active TSS	Fetal Kidney	kidney
14	chr13:49548800-49552200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr13:49548800-49552200	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr13:49548800-49552400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr13:49548800-49552400	Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr13:49548800-49552400	Active TSS	Stomach Smooth Muscle	stomach
19	chr13:49548800-49552600	Active TSS	Fetal Intestine Large	intestine
20	chr13:49548800-49552600	Active TSS	NHDF-Ad	bronchial
21	chr13:49548800-49552800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr13:49548800-49553000	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr13:49548800-49554800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr13:49548800-49555800	Active TSS	Right Ventricle	heart
25	chr13:49549000-49549600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr13:49549000-49549600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr13:49549000-49549600	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr13:49549000-49549600	Flanking Active TSS	Liver	Liver
29	chr13:49549000-49549600	ZNF genes & repeats	NHEK	skin
30	chr13:49549000-49549800	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr13:49549000-49549800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr13:49549000-49549800	Flanking Active TSS	Placenta	Placenta
33	chr13:49549000-49549800	Flanking Active TSS	HUVEC	blood vessel
34	chr13:49549000-49549800	Flanking Active TSS	NH-A	brain
35	chr13:49549000-49550000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr13:49549000-49550200	Active TSS	Right Atrium	heart
37	chr13:49549000-49551800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr13:49549000-49552000	Active TSS	Fetal Intestine Small	intestine
39	chr13:49549000-49552000	Active TSS	Osteobl	bone
40	chr13:49549000-49552200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:49549000-49552400	Active TSS	NHLF	lung
42	chr13:49549000-49552600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr13:49549000-49553200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:49549000-49553800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr13:49549000-49554200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr13:49549200-49549600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:49549200-49549600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:49549200-49549600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr13:49549200-49549600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr13:49549200-49549600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin

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