Variant report

Variant	rs537472487
Chromosome Location	chr2:234474825-234474826
allele	A/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	POLR2A	chr2:234474767-234475603	GM12878	blood:	n/a	n/a
2	SP1	chr2:234474627-234475749	A549	lung:	n/a	chr2:234474804-234474818 chr2:234474797-234474811 chr2:234474823-234474832
3	POLR2A	chr2:234474254-234475647	HepG2	liver:	n/a	n/a
4	CHD1	chr2:234474588-234475413	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:234474753-234474998	SK-N-SH	brain:	n/a	n/a
6	YY1	chr2:234474673-234475678	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr2:234474713-234475674	GM12878	blood:	n/a	n/a
8	GATA3	chr2:234474740-234475728	A549	lung:	n/a	n/a
9	POLR2A	chr2:234474632-234475690	GM12892	blood:	n/a	n/a
10	POLR2A	chr2:234474447-234475627	IMR90	lung:	n/a	n/a
11	MTA3	chr2:234474700-234475664	GM12878	blood:	n/a	n/a
12	POLR2A	chr2:234474765-234475001	A549	lung:	n/a	n/a
13	POLR2A	chr2:234474509-234475727	GM19193	blood:	n/a	n/a
14	MBD4	chr2:234474805-234475537	HepG2	liver:	n/a	n/a
15	HEY1	chr2:234474806-234475548	HepG2	liver:	n/a	chr2:234475308-234475323 chr2:234475462-234475477 chr2:234475464-234475479
16	POLR2A	chr2:234474624-234475742	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr2:234474814-234474983	GM12891	blood:	n/a	n/a
18	POLR2A	chr2:234474769-234475654	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr2:234474394-234475654	HCT-116	colon:	n/a	n/a
20	POLR2A	chr2:234474708-234475673	GM12878	blood:	n/a	n/a
21	MBD4	chr2:234474801-234475667	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:234474373-234475708	U87	brain:	n/a	n/a
23	POLR2A	chr2:234474722-234475722	K562	blood:	n/a	n/a
24	ZNF384	chr2:234474278-234475218	GM12878	blood:	n/a	n/a
25	POLR2A	chr2:234474746-234475705	MCF-7	breast:	n/a	n/a
26	POLR2A	chr2:234474697-234475638	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr2:234474718-234475632	K562	blood:	n/a	n/a
28	CHD2	chr2:234474405-234475666	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:234474265-234475656	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr2:234474387-234475589	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:234474311-234475729	GM18951	blood:	n/a	n/a
32	TCF12	chr2:234474751-234475542	A549	lung:	n/a	n/a
33	POLR2A	chr2:234474763-234475619	NB4	blood:	n/a	n/a
34	YY1	chr2:234474799-234475668	SK-N-SH	brain:	n/a	n/a
35	HCFC1	chr2:234474444-234475669	K562	blood:	n/a	n/a
36	POLR2A	chr2:234474690-234475136	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr2:234474416-234475731	GM19099	blood:	n/a	n/a
38	JUND	chr2:234474495-234475624	K562	blood:	n/a	chr2:234475583-234475591
39	MAZ	chr2:234474428-234475653	K562	blood:	n/a	chr2:234474801-234474811
40	POLR2A	chr2:234474681-234475659	GM18526	blood:	n/a	n/a
41	SIN3A	chr2:234474285-234475629	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr2:234474679-234475675	A549	lung:	n/a	chr2:234474801-234474811
43	ELK1	chr2:234474588-234474957	GM12878	blood:	n/a	n/a
44	IRF1	chr2:234474597-234475632	K562	blood:	n/a	n/a
45	YY1	chr2:234474709-234475610	GM12892	blood:	n/a	n/a
46	POLR2A	chr2:234474460-234475748	K562	blood:	n/a	n/a
47	SP1	chr2:234474628-234475760	A549	lung:	n/a	chr2:234474804-234474818 chr2:234474797-234474811 chr2:234474823-234474832
48	TBP	chr2:234474237-234475560	GM12878	blood:	n/a	n/a
49	POLR2A	chr2:234472877-234475700	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr2:234474820-234475668	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:234452682..234455147-chr2:234473464..234475374,2	MCF-7	breast:
2	chr2:234473931..234475939-chr2:234762064..234763860,2	K562	blood:
3	chr2:234473282..234477495-chr2:234598048..234603332,9	MCF-7	breast:
4	chr2:234474046..234476375-chr2:234618981..234621894,3	MCF-7	breast:
5	chr2:234400872..234402381-chr2:234473582..234476254,2	MCF-7	breast:
6	chr2:234393753..234400835-chr2:234472864..234476478,8	MCF-7	breast:
7	chr2:234389092..234391362-chr2:234473035..234476486,3	MCF-7	breast:
8	chr2:234472037..234477650-chr2:234599067..234602356,8	MCF-7	breast:

Variant related genes	Relation type
USP40	TF binding region
ENSG00000240224	Chromatin interaction
ENSG00000123485	Chromatin interaction
ENSG00000271639	Chromatin interaction
ENSG00000085982	Chromatin interaction
ENSG00000167165	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	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv876013	chr2:234338227-234579915	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv519876	chr2:234466843-234493048	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	esv3354779	chr2:234474774-234478122	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234474000-234475600	Active TSS	Fetal Brain Male	brain
2	chr2:234474000-234475800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:234474000-234475800	Active TSS	Right Atrium	heart
4	chr2:234474000-234475800	Active TSS	Stomach Smooth Muscle	stomach
5	chr2:234474200-234475000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:234474200-234475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr2:234474200-234475400	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr2:234474200-234475600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:234474200-234475600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:234474200-234475800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:234474200-234475800	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr2:234474200-234475800	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr2:234474200-234475800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:234474200-234475800	Active TSS	Fetal Intestine Small	intestine
15	chr2:234474200-234475800	Active TSS	Psoas Muscle	Psoas
16	chr2:234474200-234475800	Active TSS	Thymus	Thymus
17	chr2:234474400-234475000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr2:234474400-234475000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:234474400-234475000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
20	chr2:234474400-234475000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr2:234474400-234475000	Flanking Active TSS	HUVEC	blood vessel
22	chr2:234474400-234475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:234474400-234475400	Active TSS	Aorta	Aorta
24	chr2:234474400-234475400	Active TSS	Liver	Liver
25	chr2:234474400-234475400	Active TSS	Fetal Heart	heart
26	chr2:234474400-234475600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:234474400-234475600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:234474400-234475600	Active TSS	Colon Smooth Muscle	Colon
29	chr2:234474400-234475600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr2:234474400-234475600	Active TSS	Lung	lung
31	chr2:234474400-234475600	Active TSS	Ovary	ovary
32	chr2:234474400-234475600	Active TSS	Placenta Amnion	Placenta Amnion
33	chr2:234474400-234475600	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr2:234474400-234475600	Active TSS	GM12878-XiMat	blood
35	chr2:234474400-234475600	Active TSS	HSMMtube	muscle
36	chr2:234474400-234475800	Active TSS	H1 Cell Line	embryonic stem cell
37	chr2:234474400-234475800	Active TSS	H9 Cell Line	embryonic stem cell
38	chr2:234474400-234475800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:234474400-234475800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:234474400-234475800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:234474400-234475800	Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr2:234474400-234475800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:234474400-234475800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:234474400-234475800	Active TSS	Colonic Mucosa	Colon
45	chr2:234474400-234475800	Active TSS	Fetal Intestine Large	intestine
46	chr2:234474400-234475800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr2:234474400-234475800	Active TSS	Fetal Muscle Trunk	muscle
48	chr2:234474400-234475800	Active TSS	Fetal Muscle Leg	muscle
49	chr2:234474400-234475800	Active TSS	Fetal Stomach	stomach
50	chr2:234474400-234475800	Active TSS	Rectal Smooth Muscle	rectum

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