Variant report

Variant	rs575413492
Chromosome Location	chr2:111878557-111878558
allele	-/GCCGCCGCCGCCGCCGCC
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	POLR2A	chr2:111877810-111878697	A549	lung:	n/a	n/a
2	POLR2A	chr2:111877869-111878790	HCT-116	colon:	n/a	n/a
3	E2F6	chr2:111877408-111879340	K562	blood:	n/a	chr2:111878414-111878423 chr2:111877747-111877759 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111878285-111878294 chr2:111878171-111878181
4	PAX5	chr2:111878278-111879229	GM12878	blood:	n/a	chr2:111878388-111878397 chr2:111879173-111879182 chr2:111879020-111879029
5	MYBL2	chr2:111877719-111878714	HepG2	liver:	n/a	n/a
6	TAF1	chr2:111877903-111878737	A549	lung:	n/a	n/a
7	MAX	chr2:111877563-111881015	NB4	blood:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
8	MAX	chr2:111877317-111879304	H1-hESC	embryonic stem cell:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111877479-111877489 chr2:111879218-111879227
9	ELK1	chr2:111878346-111878857	GM12878	blood:	n/a	n/a
10	E2F6	chr2:111876311-111880584	H1-hESC	embryonic stem cell:	n/a	chr2:111876443-111876455 chr2:111878414-111878423 chr2:111880549-111880558 chr2:111880095-111880104 chr2:111877747-111877759 chr2:111877347-111877357 chr2:111876622-111876632 chr2:111877478-111877490 chr2:111878679-111878691 chr2:111877963-111877973 chr2:111880318-111880330 chr2:111878285-111878294 chr2:111878171-111878181 chr2:111880053-111880060
11	POLR2A	chr2:111877782-111879129	MCF-7	breast:	n/a	n/a
12	CREB1	chr2:111877860-111878690	A549	lung:	n/a	n/a
13	TAF1	chr2:111878365-111878654	H1-neurons	neurons:	n/a	n/a
14	EP300	chr2:111877870-111878996	SK-N-SH	brain:	n/a	chr2:111878469-111878485 chr2:111878110-111878126 chr2:111878390-111878406 chr2:111878168-111878177 chr2:111878159-111878175 chr2:111878171-111878180
15	CREB1	chr2:111878014-111878911	K562	blood:	n/a	n/a
16	MAX	chr2:111877825-111879196	SK-N-SH	brain:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693
17	PML	chr2:111877945-111878708	K562	blood:	n/a	n/a
18	TCF12	chr2:111877680-111880212	A549	lung:	n/a	n/a
19	SIN3AK20	chr2:111877611-111881217	MCF-7	breast:	n/a	n/a
20	RCOR1	chr2:111877851-111878973	HepG2	liver:	n/a	n/a
21	TAF7	chr2:111878146-111878623	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr2:111877835-111878982	PFSK-1	brain:	n/a	n/a
23	REST	chr2:111878343-111878731	SK-N-SH	brain:	n/a	n/a
24	PAX5	chr2:111878336-111879403	GM12878	blood:	n/a	chr2:111878388-111878397 chr2:111879173-111879182 chr2:111879020-111879029
25	TCF12	chr2:111877517-111879634	ECC-1	luminal epithelium:	n/a	n/a
26	TBP	chr2:111878206-111878641	Hela-S3	cervix:	n/a	n/a
27	NR2F2	chr2:111877591-111878775	MCF-7	breast:	n/a	n/a
28	POLR2A	chr2:111878137-111878791	SK-N-MC	brain:	n/a	n/a
29	POLR2A	chr2:111877971-111878943	HCT-116	colon:	n/a	n/a
30	MYBL2	chr2:111877844-111878570	HepG2	liver:	n/a	n/a
31	POLR2A	chr2:111877945-111878731	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr2:111877806-111880414	GM12878	blood:	n/a	n/a
33	HCFC1	chr2:111877979-111880854	K562	blood:	n/a	n/a
34	POLR2A	chr2:111877738-111878830	K562	blood:	n/a	n/a
35	POLR2A	chr2:111877942-111881067	IMR90	lung:	n/a	n/a
36	POLR2A	chr2:111877963-111879180	K562	blood:	n/a	n/a
37	STAT1	chr2:111877756-111878558	GM12878	blood:	n/a	n/a
38	IRF1	chr2:111878028-111878677	K562	blood:	n/a	chr2:111878413-111878427 chr2:111878485-111878496 chr2:111878397-111878411
39	POU2F2	chr2:111878273-111878633	GM12878	blood:	n/a	n/a
40	MAFK	chr2:111878374-111878894	IMR90	lung:	n/a	n/a
41	TBP	chr2:111878293-111878731	GM12878	blood:	n/a	n/a
42	YY1	chr2:111877944-111878574	K562	blood:	n/a	chr2:111878164-111878173 chr2:111878499-111878510 chr2:111878164-111878175 chr2:111878165-111878179 chr2:111878414-111878423 chr2:111878039-111878050 chr2:111878168-111878182 chr2:111878285-111878299 chr2:111878170-111878179 chr2:111878159-111878173 chr2:111878164-111878178
43	POLR2A	chr2:111878330-111878558	GM12891	blood:	n/a	n/a
44	MAX	chr2:111877542-111881163	HepG2	liver:	n/a	chr2:111878235-111878244 chr2:111878233-111878243 chr2:111878683-111878693 chr2:111879218-111879227
45	TAF1	chr2:111877857-111878785	K562	blood:	n/a	n/a
46	POLR2A	chr2:111877432-111881054	K562	blood:	n/a	n/a
47	TAF1	chr2:111878268-111878639	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr2:111878117-111879345	H1-neurons	neurons:	n/a	n/a
49	GATA3	chr2:111877704-111879021	A549	lung:	n/a	n/a
50	RELA	chr2:111878176-111879100	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:111869458..111872537-chr2:111876483..111880583,5	MCF-7	breast:
2	chr2:111877393..111879713-chr2:112235053..112237981,2	K562	blood:
3	chr2:111434111..111436826-chr2:111878321..111880919,2	K562	blood:
4	chr17:39845098..39845687-chr2:111878260..111879017,2	Hela-S3	cervix:
5	chr2:111878400..111878946-chr7:25164305..25164896,2	HCT-116	colon:
6	chr2:111878015..111878894-chr21:30391308..30391895,2	Hela-S3	cervix:
7	chr19:58897967..58899180-chr2:111878320..111878941,3	HCT-116	colon:
8	chr1:144533704..144534633-chr2:111878333..111878839,2	Hela-S3	cervix:
9	chr2:111876826..111879311-chr2:111966028..111968773,2	K562	blood:
10	chr12:28120103..28122878-chr2:111877498..111879183,2	MCF-7	breast:

Variant related genes	Relation type
BCL2L11	TF binding region
ENSG00000172965	Chromatin interaction
ENSG00000156253	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000266640	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000087494	Chromatin interaction
ENSG00000083845	Chromatin interaction
ENSG00000172115	Chromatin interaction
ENSG00000204581	Chromatin interaction
ENSG00000169679	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv834331	chr2:111812139-112004678	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv874842	chr2:111870220-111892984	Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv829618	chr2:111875627-111881547	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	esv3338590	chr2:111876081-111880479	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv3373707	chr2:111877306-111879854	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 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	chr2:111874400-111879800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr2:111874800-111879600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:111874800-111880000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:111875200-111880000	Bivalent Enhancer	Fetal Brain Male	brain
5	chr2:111875600-111880000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr2:111875600-111881200	Active TSS	Psoas Muscle	Psoas
7	chr2:111876200-111880000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:111876400-111880000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:111877000-111881000	Active TSS	Small Intestine	intestine
10	chr2:111877000-111881400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:111877200-111879200	Active TSS	Rectal Smooth Muscle	rectum
12	chr2:111877200-111880800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
13	chr2:111877400-111879200	Transcr. at gene 5' and 3'	Right Atrium	heart
14	chr2:111877600-111879200	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:111877600-111879200	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr2:111877600-111879400	Active TSS	HSMM	muscle
17	chr2:111877600-111879800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:111877600-111881000	Active TSS	Esophagus	oesophagus
19	chr2:111877600-111881200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:111877600-111881200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:111877600-111881400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:111877800-111878600	Active TSS	HepG2	liver
23	chr2:111877800-111879000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:111877800-111879200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr2:111877800-111879200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:111877800-111879200	Active TSS	Brain Angular Gyrus	brain
27	chr2:111877800-111879200	Active TSS	Placenta Amnion	Placenta Amnion
28	chr2:111877800-111879200	Active TSS	K562	blood
29	chr2:111877800-111879400	Active TSS	Fetal Heart	heart
30	chr2:111877800-111880000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr2:111877800-111880800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:111877800-111881000	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr2:111877800-111881000	Active TSS	A549	lung
34	chr2:111877800-111881000	Active TSS	Hela-S3	cervix
35	chr2:111877800-111881200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr2:111877800-111881400	Active TSS	Ovary	ovary
37	chr2:111877800-111881400	Active TSS	HSMMtube	muscle
38	chr2:111878000-111878600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
39	chr2:111878000-111878800	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:111878000-111878800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr2:111878000-111878800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:111878000-111878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr2:111878000-111878800	Active TSS	Colon Smooth Muscle	Colon
44	chr2:111878000-111878800	Active TSS	Placenta	Placenta
45	chr2:111878000-111879000	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
46	chr2:111878000-111879000	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
47	chr2:111878000-111879000	Bivalent/Poised TSS	Fetal Stomach	stomach
48	chr2:111878000-111879200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:111878000-111879200	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr2:111878000-111879200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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