Variant report

Variant	rs190634663
Chromosome Location	chr2:48009721-48009722
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	GABPA	chr2:48009709-48010568	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:48009717-48010552	SK-N-SH	brain:	n/a	n/a
3	SIN3AK20	chr2:48009451-48011776	MCF-7	breast:	n/a	n/a
4	SMC3	chr2:48009518-48010524	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr2:48009607-48009851	HepG2	liver:	n/a	n/a
6	MAX	chr2:48009528-48011580	NB4	blood:	n/a	chr2:48011032-48011042
7	POLR2A	chr2:48009627-48011001	HL-60	blood:	n/a	n/a
8	POLR2A	chr2:48009642-48010925	U87	brain:	n/a	n/a
9	POLR2A	chr2:48009488-48011430	HepG2	liver:	n/a	n/a
10	JUND	chr2:48009510-48010538	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAFK	chr2:48009618-48009842	HepG2	liver:	n/a	chr2:48009779-48009793 chr2:48009780-48009796 chr2:48009781-48009792 chr2:48009781-48009792
12	FOXM1	chr2:48009670-48010610	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:48009672-48010122	H1-hESC	embryonic stem cell:	n/a	n/a
14	MBD4	chr2:48009392-48009994	HepG2	liver:	n/a	n/a
15	REST	chr2:48009658-48010636	HepG2	liver:	n/a	chr2:48010029-48010042
16	BHLHE40	chr2:48009535-48010884	K562	blood:	n/a	n/a
17	POLR2A	chr2:48009717-48010617	ECC-1	luminal epithelium:	n/a	n/a
18	CHD2	chr2:48009671-48010970	HepG2	liver:	n/a	chr2:48010273-48010283
19	SP1	chr2:48009715-48010611	H1-hESC	embryonic stem cell:	n/a	chr2:48010130-48010140 chr2:48010157-48010166 chr2:48010129-48010141 chr2:48009881-48009888 chr2:48010129-48010140 chr2:48010130-48010140 chr2:48010156-48010167 chr2:48010156-48010168 chr2:48010156-48010168 chr2:48010130-48010139 chr2:48010130-48010139 chr2:48010131-48010140 chr2:48010157-48010171 chr2:48010046-48010060 chr2:48010129-48010141 chr2:48010130-48010144 chr2:48010224-48010245 chr2:48010187-48010198
20	MYC	chr2:48009537-48011035	A549	lung:	n/a	n/a
21	POLR2A	chr2:48009321-48010999	Hela-S3	cervix:	n/a	n/a
22	EP300	chr2:48009619-48010969	ECC-1	luminal epithelium:	n/a	n/a
23	BCLAF1	chr2:48009585-48010673	GM12878	blood:	n/a	n/a
24	POLR2A	chr2:48009656-48010632	PBDE	blood:	n/a	n/a
25	POLR2A	chr2:48009627-48011455	K562	blood:	n/a	n/a
26	E2F6	chr2:48009686-48011751	A549	lung:	n/a	chr2:48010286-48010295 chr2:48011052-48011064 chr2:48010287-48010294 chr2:48010235-48010244 chr2:48010287-48010294 chr2:48009932-48009941 chr2:48011044-48011053 chr2:48010285-48010296 chr2:48010286-48010294 chr2:48010750-48010759 chr2:48010286-48010298 chr2:48010287-48010294 chr2:48011131-48011140
27	POLR2A	chr2:48009691-48011296	GM18526	blood:	n/a	n/a
28	RELA	chr2:48009631-48010639	GM12891	blood:	n/a	n/a
29	MAX	chr2:48009393-48010957	Hela-S3	cervix:	n/a	n/a
30	EGR1	chr2:48009700-48010541	MCF-7	breast:	n/a	chr2:48009933-48009946 chr2:48010088-48010102 chr2:48010099-48010109
31	POLR2A	chr2:48009667-48011276	HepG2	liver:	n/a	n/a
32	ZKSCAN1	chr2:48009499-48010537	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr2:48009704-48011601	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr2:48009620-48011271	GM18505	blood:	n/a	n/a
35	POLR2A	chr2:48009647-48011413	K562	blood:	n/a	n/a
36	RFX5	chr2:48009528-48010488	HepG2	liver:	n/a	chr2:48010064-48010072 chr2:48009782-48009790
37	POLR2A	chr2:48009501-48010642	Hela-S3	cervix:	n/a	n/a
38	ZBTB7A	chr2:48009699-48010230	ECC-1	luminal epithelium:	n/a	n/a
39	REST	chr2:48009460-48011268	H1-neurons	neurons:	n/a	chr2:48010029-48010042
40	CEBPB	chr2:48009521-48009987	IMR90	lung:	n/a	n/a
41	RCOR1	chr2:48009681-48010582	GM12878	blood:	n/a	n/a
42	RCOR1	chr2:48009401-48010939	Hela-S3	cervix:	n/a	n/a
43	ELK1	chr2:48009694-48010621	Hela-S3	cervix:	n/a	n/a
44	WRNIP1	chr2:48009588-48009978	GM12878	blood:	n/a	n/a
45	ELF1	chr2:48009714-48010354	K562	blood:	n/a	n/a
46	BHLHE40	chr2:48009638-48010632	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:48009547-48011872	Hela-S3	cervix:	n/a	n/a
48	HCFC1	chr2:48009441-48011000	Hela-S3	cervix:	n/a	n/a
49	MAX	chr2:48009475-48011647	HepG2	liver:	n/a	chr2:48011032-48011042
50	STAT5A	chr2:48009534-48009891	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48009698-48009748	HEEpiC	esophagus:	n/a
2	chr2:48009698-48009748	HCF	heart:	n/a
3	chr2:48009698-48009748	A549	lung:	n/a
4	chr2:48009698-48009748	GM06990	blood:	n/a
5	chr2:48009698-48009748	HepG2	liver:	n/a
6	chr2:48009698-48009748	HRPEpiC	eye:	n/a
7	chr2:48009698-48009748	NB4	blood:	n/a
8	chr2:48009698-48009748	AG10803	skin:	n/a
9	chr2:48009698-48009748	NHBE	bronchial:	n/a
10	chr2:48009698-48009748	T-47D	breast:	n/a
11	chr2:48009698-48009748	HL-60	blood:	n/a
12	chr2:48009698-48009748	H1-hESC	embryonic stem cell:	embryo
13	chr2:48009698-48009748	HRE	kidney:	n/a
14	chr2:48009698-48009748	MCF-7	breast:	n/a
15	chr2:48009698-48009748	HMEC	breast:	n/a
16	chr2:48009698-48009748	ECC-1	luminal epithelium:	n/a
17	chr2:48009698-48009748	Jurkat	blood:	n/a
18	chr2:48009698-48009748	MCF10A-Er-Src	breast:	n/a
19	chr2:48009698-48009748	HRCEpiC	kidney:	n/a
20	chr2:48009698-48009748	SKMC	muscle:	n/a
21	chr2:48009698-48009748	HEK293	kidney:	embryo
22	chr2:48009698-48009748	CMK	blood:	n/a
23	chr2:48009698-48009748	NH-A	brain:	n/a
24	chr2:48009698-48009748	SK-N-SH_RA	brain:	n/a
25	chr2:48009698-48009748	NT2-D1	testis:	n/a
26	chr2:48009698-48009748	AG04449	skin:	fetal
27	chr2:48009698-48009748	Hela-S3	cervix:	n/a
28	chr2:48009698-48009748	GM19239	blood:	n/a
29	chr2:48009698-48009748	GM12892	blood:	n/a
30	chr2:48009698-48009748	AoSMC	blood vessel:	n/a
31	chr2:48009698-48009748	HUVEC	blood vessel:	n/a
32	chr2:48009698-48009748	Caco-2	colon:	n/a
33	chr2:48009698-48009748	ProgFib	skin:	n/a
34	chr2:48009698-48009748	K562	blood:	n/a
35	chr2:48009698-48009748	HCPEpiC	choroid plexus:	n/a
36	chr2:48009698-48009748	PrEC	prostate:	n/a
37	chr2:48009698-48009748	SK-N-SH	brain:	n/a
38	chr2:48009698-48009748	HCT-116	colon:	n/a
39	chr2:48009698-48009748	U87	brain:	n/a
40	chr2:48009698-48009748	HNPCEpiC	eye:	n/a
41	chr2:48009698-48009748	BE2_C	brain:	n/a
42	chr2:48009698-48009748	GM12878	blood:	n/a
43	chr2:48009698-48009748	AG09319	gingival:	n/a
44	chr2:48009698-48009748	PFSK-1	brain:	n/a
45	chr2:48009698-48009748	HIPEpiC	eye:	n/a
46	chr2:48009698-48009748	GM12891	blood:	n/a
47	chr2:48009698-48009748	RPTEC	kidney:	n/a
48	chr2:48009698-48009748	LNCaP	prostate:	n/a
49	chr2:48009698-48009748	BJ	skin:	n/a
50	chr2:48009698-48009748	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48008927..48012318-chr2:48131369..48134669,5	MCF-7	breast:
2	chr2:47629900..47631449-chr2:48009384..48011204,2	K562	blood:
3	chr16:27279521..27280140-chr2:48009595..48010496,2	Hela-S3	cervix:
4	chr2:48009680..48011593-chr2:48034365..48037361,4	K562	blood:
5	chr2:48008730..48016091-chr2:48023378..48031018,13	K562	blood:
6	chr2:48009330..48011315-chr2:48667151..48669363,2	MCF-7	breast:
7	chr1:17231455..17232098-chr2:48009621..48010207,2	Hela-S3	cervix:
8	chr2:47400478..47403818-chr2:48008752..48011597,4	K562	blood:
9	chr2:48009081..48011260-chr2:48666512..48669305,2	K562	blood:
10	chr2:48009241..48011521-chr2:48133698..48136009,2	K562	blood:
11	chr2:48009564..48012056-chr2:48131613..48133953,3	MCF-7	breast:

Variant related genes	Relation type
MSH6	TF binding region
MSH6	CpG island
ENSG00000143933	Chromatin interaction
ENSG00000138081	Chromatin interaction
ENSG00000245888	Chromatin interaction
ENSG00000235369	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000272663	Chromatin interaction
ENSG00000169189	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

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	nsv873999	chr2:47916074-48019485	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv998096	chr2:47939614-48131697	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1009769	chr2:47972642-48509765	Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv535680	chr2:47972642-48509765	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats 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	36 gene(s)	inside rSNPs	diseases
5	esv3392564	chr2:48009598-48012596	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	17 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	chr2:48008400-48011400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr2:48009000-48009800	Flanking Active TSS	Hela-S3	cervix
3	chr2:48009000-48011400	Active TSS	Rectal Smooth Muscle	rectum
4	chr2:48009000-48012400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:48009200-48009800	Flanking Active TSS	Liver	Liver
6	chr2:48009200-48009800	Flanking Active TSS	Placenta	Placenta
7	chr2:48009200-48010000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:48009200-48012000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:48009200-48012200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:48009200-48012400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:48009200-48012600	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:48009200-48012800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:48009200-48012800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr2:48009400-48009800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:48009400-48009800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:48009400-48009800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
17	chr2:48009400-48009800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:48009400-48009800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr2:48009400-48009800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:48009400-48009800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr2:48009400-48009800	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr2:48009400-48009800	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr2:48009400-48009800	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr2:48009400-48009800	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr2:48009400-48009800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr2:48009400-48009800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr2:48009400-48009800	Flanking Active TSS	Fetal Intestine Large	intestine
28	chr2:48009400-48009800	Flanking Active TSS	Fetal Thymus	thymus
29	chr2:48009400-48009800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr2:48009400-48009800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr2:48009400-48009800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr2:48009400-48009800	Flanking Active TSS	GM12878-XiMat	blood
33	chr2:48009400-48009800	Flanking Active TSS	K562	blood
34	chr2:48009400-48009800	Flanking Active TSS	NH-A	brain
35	chr2:48009400-48009800	Flanking Active TSS	Osteobl	bone
36	chr2:48009400-48010000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr2:48009400-48010000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr2:48009400-48010000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr2:48009400-48010000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr2:48009400-48010000	Flanking Active TSS	Dnd41	blood
41	chr2:48009400-48010000	Flanking Active TSS	HMEC	breast
42	chr2:48009400-48010000	Flanking Active TSS	HUVEC	blood vessel
43	chr2:48009400-48010000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr2:48009400-48010600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr2:48009400-48011000	Bivalent/Poised TSS	HepG2	liver
46	chr2:48009400-48011400	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr2:48009400-48011400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:48009400-48011400	Active TSS	Stomach Smooth Muscle	stomach
49	chr2:48009400-48011600	Active TSS	Brain Anterior Caudate	brain
50	chr2:48009400-48011600	Active TSS	Brain Substantia Nigra	brain

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