Variant report

Variant	rs12478635
Chromosome Location	chr2:209120258-209120259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:397)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:397 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr2:209120092-209120292	GM12878	blood:	n/a	n/a
2	FOXP2	chr2:209119786-209120301	PFSK-1	brain:	n/a	n/a
3	CTCF	chr2:209120160-209120310	GM12867	blood:	n/a	n/a
4	POLR2A	chr2:209118794-209120329	GM19193	blood:	n/a	n/a
5	HNF4G	chr2:209119565-209120356	HepG2	liver:	n/a	n/a
6	YY1	chr2:209119568-209120634	SK-N-SH	brain:	n/a	chr2:209119879-209119888
7	MXI1	chr2:209118476-209120613	HepG2	liver:	n/a	n/a
8	CTCF	chr2:209120140-209120290	BJ	skin:	n/a	n/a
9	YY1	chr2:209119646-209120432	ECC-1	luminal epithelium:	n/a	chr2:209119879-209119888
10	CTCF	chr2:209120160-209120310	HRPEpiC	eye:	n/a	n/a
11	BHLHE40	chr2:209118758-209120311	GM12878	blood:	n/a	n/a
12	RCOR1	chr2:209119896-209120303	GM12878	blood:	n/a	n/a
13	CTCF	chr2:209120140-209120290	HVMF	connective:	n/a	n/a
14	POLR2A	chr2:209118690-209120631	HepG2	liver:	n/a	n/a
15	JUND	chr2:209119967-209120294	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr2:209118607-209120327	K562	blood:	n/a	n/a
17	MTA3	chr2:209118992-209120722	GM12878	blood:	n/a	n/a
18	IRF1	chr2:209119615-209120302	K562	blood:	n/a	chr2:209119847-209119861 chr2:209119943-209119957 chr2:209119875-209119889
19	ARID3A	chr2:209120006-209120432	K562	blood:	n/a	n/a
20	CTCF	chr2:209120020-209120337	GM19239	blood:	n/a	n/a
21	EBF1	chr2:209119605-209120307	GM12878	blood:	n/a	chr2:209119915-209119928
22	ELF1	chr2:209119634-209120360	HepG2	liver:	n/a	n/a
23	CTCF	chr2:209119933-209120353	MCF-7	breast:	n/a	n/a
24	REST	chr2:209118863-209120379	H1-neurons	neurons:	n/a	chr2:209119866-209119879
25	CTCF	chr2:209120120-209120270	NHEK	skin:	n/a	n/a
26	RCOR1	chr2:209118644-209120330	Hela-S3	cervix:	n/a	n/a
27	PML	chr2:209119600-209120422	K562	blood:	n/a	n/a
28	POLR2A	chr2:209118834-209120397	HEK293	kidney:	n/a	n/a
29	POLR2A	chr2:209118485-209120368	K562	blood:	n/a	n/a
30	RCOR1	chr2:209119833-209120485	IMR90	lung:	n/a	n/a
31	TEAD4	chr2:209118072-209120414	HepG2	liver:	n/a	n/a
32	CTCF	chr2:209120180-209120330	HA-sp	spinal cord:	n/a	n/a
33	HNF4A	chr2:209119879-209120321	HepG2	liver:	n/a	n/a
34	CTCF	chr2:209120086-209120348	GM19240	blood:	n/a	n/a
35	YY1	chr2:209119565-209120370	SK-N-SH_RA	brain:	n/a	chr2:209119879-209119888
36	POLR2A	chr2:209119487-209120362	PANC-1	pancreas:	n/a	n/a
37	YY1	chr2:209119488-209120497	HepG2	liver:	n/a	chr2:209119879-209119888
38	RAD21	chr2:209119771-209120463	A549	lung:	n/a	n/a
39	TAF1	chr2:209119541-209120325	HepG2	liver:	n/a	n/a
40	RAD21	chr2:209119806-209120401	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr2:209118673-209120366	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr2:209119512-209120287	SK-N-SH	brain:	n/a	n/a
43	NFIC	chr2:209118472-209120400	HepG2	liver:	n/a	n/a
44	TAF1	chr2:209119493-209120580	HepG2	liver:	n/a	n/a
45	RELA	chr2:209118515-209120334	GM15510	blood:	n/a	n/a
46	CTCF	chr2:209119907-209120319	Kidney_OC	kidney:	n/a	n/a
47	CUX1	chr2:209119970-209120273	K562	blood:	n/a	n/a
48	CTCF	chr2:209120120-209120270	AoAF	blood vessel:	n/a	n/a
49	CTCF	chr2:209119971-209120353	ProgFib	skin:	n/a	n/a
50	YY1	chr2:209119565-209120392	GM12892	blood:	n/a	chr2:209119879-209119888

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:209120237-209120287	T-47D	breast:	n/a
2	chr2:209120237-209120287	HepG2	liver:	n/a
3	chr2:209120237-209120287	ovcar-3	ovarian:	n/a
4	chr2:209120237-209120287	AG09309	skin:	n/a
5	chr2:209120237-209120287	U87	brain:	n/a
6	chr2:209120237-209120287	NHDF-neo	bronchial:	n/a
7	chr2:209120237-209120287	GM12892	blood:	n/a
8	chr2:209120237-209120287	HL-60	blood:	n/a
9	chr2:209120237-209120287	PANC-1	pancreas:	n/a
10	chr2:209120237-209120287	HRE	kidney:	n/a
11	chr2:209120237-209120287	HRPEpiC	eye:	n/a
12	chr2:209120237-209120287	SK-N-SH	brain:	n/a
13	chr2:209120237-209120287	HCPEpiC	choroid plexus:	n/a
14	chr2:209120237-209120287	HUVEC	blood vessel:	n/a
15	chr2:209120237-209120287	HPAEpiC	pulmonary alveolar:	n/a
16	chr2:209120237-209120287	Caco-2	colon:	n/a
17	chr2:209120237-209120287	BJ	skin:	n/a
18	chr2:209120237-209120287	NHBE	bronchial:	n/a
19	chr2:209120237-209120287	LNCaP	prostate:	n/a
20	chr2:209120237-209120287	HNPCEpiC	eye:	n/a
21	chr2:209120237-209120287	Hepatocyte	liver:	n/a
22	chr2:209120237-209120287	CMK	blood:	n/a
23	chr2:209120237-209120287	SAEC	small airway:	n/a
24	chr2:209120237-209120287	ECC-1	luminal epithelium:	n/a
25	chr2:209120237-209120287	PFSK-1	brain:	n/a
26	chr2:209120237-209120287	AG10803	skin:	n/a
27	chr2:209120237-209120287	GM12878	blood:	n/a
28	chr2:209120237-209120287	GM12891	blood:	n/a
29	chr2:209120237-209120287	MCF10A-Er-Src	breast:	n/a
30	chr2:209120237-209120287	HCM	heart:	n/a
31	chr2:209120237-209120287	GM19239	blood:	n/a
32	chr2:209120237-209120287	SK-N-SH_RA	brain:	n/a
33	chr2:209120237-209120287	PrEC	prostate:	n/a
34	chr2:209120237-209120287	HEEpiC	esophagus:	n/a
35	chr2:209120237-209120287	HRCEpiC	kidney:	n/a
36	chr2:209120237-209120287	HEK293	kidney:	embryo
37	chr2:209120237-209120287	K562	blood:	n/a
38	chr2:209120237-209120287	HCT-116	colon:	n/a
39	chr2:209120237-209120287	IMR90	lung:	fetal
40	chr2:209120237-209120287	BE2_C	brain:	n/a
41	chr2:209120237-209120287	AoSMC	blood vessel:	n/a
42	chr2:209120237-209120287	AG04449	skin:	fetal
43	chr2:209120237-209120287	SK-N-MC	brain:	n/a
44	chr2:209120237-209120287	GM06990	blood:	n/a
45	chr2:209120237-209120287	H1-hESC	embryonic stem cell:	embryo
46	chr2:209120237-209120287	MCF-7	breast:	n/a
47	chr2:209120237-209120287	AG04450	lung:	fetal
48	chr2:209120237-209120287	HIPEpiC	eye:	n/a
49	chr2:209120237-209120287	NB4	blood:	n/a
50	chr2:209120237-209120287	NH-A	brain:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:
2	chr2:209095163..209099233-chr2:209117961..209120869,4	K562	blood:
3	chr2:209119923..209123053-chr2:209129009..209130826,3	MCF-7	breast:
4	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
5	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
6	chr2:209118313..209121811-chr2:209130870..209135068,6	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIKFYVE-1	chr2:209120124-209120346	ENSG00000231908.1

No data

Variant related genes	Relation type
IDH1	TF binding region
IDH1	CpG island
ENSG00000115020	Chromatin interaction
ENSG00000263524	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000228380	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12617462	0.84[JPT][hapmap];1.00[YRI][hapmap]
rs1370376	0.92[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs16840781	0.82[CHB][hapmap]
rs4627502	0.93[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap]
rs56713124	0.82[EUR][1000 genomes]
rs62195266	0.82[EUR][1000 genomes]
rs7593466	0.82[CHB][hapmap]

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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer 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	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12478635	NDUFS1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209117200-209120400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:209117800-209120600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr2:209117800-209120800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:209118000-209120600	Active TSS	Ovary	ovary
5	chr2:209118000-209120600	Active TSS	Right Ventricle	heart
6	chr2:209118000-209120800	Active TSS	NHLF	lung
7	chr2:209118200-209120600	Active TSS	GM12878-XiMat	blood
8	chr2:209118200-209120800	Active TSS	H1 Cell Line	embryonic stem cell
9	chr2:209118400-209120400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:209118400-209120400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:209118400-209120400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:209118400-209120400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:209118400-209120400	Active TSS	Aorta	Aorta
14	chr2:209118400-209120400	Active TSS	Brain Angular Gyrus	brain
15	chr2:209118400-209120400	Active TSS	Small Intestine	intestine
16	chr2:209118400-209120600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:209118400-209120600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:209118400-209120600	Active TSS	Left Ventricle	heart
19	chr2:209118400-209120800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:209118400-209120800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:209118600-209120400	Active TSS	Fetal Intestine Large	intestine
22	chr2:209118600-209120400	Active TSS	Psoas Muscle	Psoas
23	chr2:209118600-209120400	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr2:209118600-209120400	Bivalent/Poised TSS	HepG2	liver
25	chr2:209118600-209120400	Active TSS	K562	blood
26	chr2:209118600-209120400	Active TSS	NHDF-Ad	bronchial
27	chr2:209118600-209120600	Active TSS	Brain Inferior Temporal Lobe	brain
28	chr2:209118600-209120600	Active TSS	Colonic Mucosa	Colon
29	chr2:209118600-209120600	Active TSS	Rectal Smooth Muscle	rectum
30	chr2:209118600-209120600	Active TSS	HSMMtube	muscle
31	chr2:209118600-209120800	Active TSS	H9 Cell Line	embryonic stem cell
32	chr2:209118600-209120800	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr2:209118600-209120800	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr2:209118600-209120800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr2:209118600-209120800	Active TSS	Fetal Brain Female	brain
36	chr2:209118600-209120800	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr2:209118600-209120800	Active TSS	A549	lung
38	chr2:209118800-209120400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:209118800-209120400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:209118800-209120400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:209118800-209120400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr2:209118800-209120400	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr2:209118800-209120400	Active TSS	Brain Anterior Caudate	brain
44	chr2:209118800-209120400	Active TSS	Brain Cingulate Gyrus	brain
45	chr2:209118800-209120400	Active TSS	Brain Hippocampus Middle	brain
46	chr2:209118800-209120400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:209118800-209120400	Active TSS	Colon Smooth Muscle	Colon
48	chr2:209118800-209120400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr2:209118800-209120400	Active TSS	Fetal Heart	heart
50	chr2:209118800-209120400	Active TSS	Gastric	stomach

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