Variant report

Variant	rs540155624
Chromosome Location	chr2:47168160-47168161
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	SP1	chr2:47167281-47168223	A549	lung:	n/a	chr2:47167597-47167606 chr2:47168108-47168117 chr2:47167596-47167608 chr2:47167925-47167937 chr2:47167925-47167937 chr2:47167596-47167608 chr2:47167598-47167607 chr2:47168104-47168118 chr2:47168107-47168119 chr2:47167927-47167936 chr2:47167597-47167606
2	POLR2A	chr2:47167999-47168637	PANC-1	pancreas:	n/a	n/a
3	E2F4	chr2:47167993-47169602	K562	blood:	n/a	chr2:47169461-47169468 chr2:47168901-47168909 chr2:47168899-47168910 chr2:47169461-47169468 chr2:47168108-47168120 chr2:47168958-47168968 chr2:47169457-47169469 chr2:47169461-47169468
4	CTCF	chr2:47168160-47168310	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:47168048-47169610	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:47168038-47169209	K562	blood:	n/a	n/a
7	TCF3	chr2:47168108-47169060	GM12878	blood:	n/a	n/a
8	TAF1	chr2:47168110-47169018	HepG2	liver:	n/a	n/a
9	CREB1	chr2:47167831-47169080	A549	lung:	n/a	chr2:47168009-47168022
10	ZBTB7A	chr2:47167608-47168272	ECC-1	luminal epithelium:	n/a	n/a
11	ZBTB7A	chr2:47167467-47169239	ECC-1	luminal epithelium:	n/a	n/a
12	POLR2A	chr2:47167486-47168583	U87	brain:	n/a	n/a
13	POLR2A	chr2:47167996-47169186	K562	blood:	n/a	n/a
14	POLR2A	chr2:47167706-47169478	HUVEC	blood vessel:	n/a	n/a
15	YY1	chr2:47168081-47169510	GM12892	blood:	n/a	chr2:47168670-47168690 chr2:47168245-47168259 chr2:47168676-47168688
16	MAX	chr2:47167603-47169355	K562	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
17	PML	chr2:47167975-47168466	K562	blood:	n/a	n/a
18	POLR2A	chr2:47167805-47169022	A549	lung:	n/a	n/a
19	MYC	chr2:47167697-47169785	NB4	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
20	POLR2A	chr2:47168032-47169485	MCF-7	breast:	n/a	n/a
21	MXI1	chr2:47166976-47169461	HepG2	liver:	n/a	n/a
22	GATA3	chr2:47167309-47169655	A549	lung:	n/a	chr2:47169431-47169439
23	YY1	chr2:47168151-47168391	HCT-116	colon:	n/a	chr2:47168245-47168259
24	ELF1	chr2:47168142-47169118	GM12878	blood:	n/a	chr2:47168240-47168252
25	CTCF	chr2:47168140-47168290	GM12866	blood:	n/a	n/a
26	MAX	chr2:47167779-47169115	HepG2	liver:	n/a	chr2:47168106-47168116 chr2:47169037-47169048
27	YY1	chr2:47167765-47169076	HepG2	liver:	n/a	chr2:47168670-47168690 chr2:47168245-47168259 chr2:47167942-47167953 chr2:47168676-47168688
28	MAX	chr2:47167138-47169869	Hela-S3	cervix:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
29	SMARCB1	chr2:47167445-47169505	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr2:47167940-47168230	GM12865	blood:	n/a	n/a
31	TAF1	chr2:47168094-47168565	H1-hESC	embryonic stem cell:	n/a	n/a
32	MYC	chr2:47167712-47169673	K562	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
33	POLR2A	chr2:47166646-47169549	HepG2	liver:	n/a	n/a
34	EP300	chr2:47167679-47168448	HepG2	liver:	n/a	chr2:47168025-47168041
35	EGR1	chr2:47167736-47168525	HCT-116	colon:	n/a	chr2:47168105-47168115 chr2:47168103-47168116 chr2:47168102-47168117 chr2:47168379-47168393 chr2:47168103-47168116
36	POLR2A	chr2:47167963-47169919	GM12892	blood:	n/a	n/a
37	POLR2A	chr2:47167989-47169640	GM10847	blood:	n/a	n/a
38	CTCF	chr2:47168080-47168230	HMEC	breast:	n/a	n/a
39	HEY1	chr2:47167857-47168559	K562	blood:	n/a	n/a
40	CTCF	chr2:47168038-47168307	K562	blood:	n/a	n/a
41	SIN3A	chr2:47167797-47169483	H1-hESC	embryonic stem cell:	n/a	chr2:47167951-47167960 chr2:47167933-47167946 chr2:47168399-47168408
42	POLR2A	chr2:47167932-47169713	GM18526	blood:	n/a	n/a
43	E2F6	chr2:47167811-47168479	K562	blood:	n/a	chr2:47168108-47168120
44	MAX	chr2:47167670-47168486	SK-N-SH	brain:	n/a	chr2:47168106-47168116 chr2:47167751-47167760
45	HEY1	chr2:47167080-47169431	HepG2	liver:	n/a	chr2:47167527-47167542
46	POLR2A	chr2:47167967-47168574	HepG2	liver:	n/a	n/a
47	ZBTB7A	chr2:47167763-47168723	K562	blood:	n/a	n/a
48	TAF1	chr2:47168105-47169146	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr2:47168094-47171520	GM12878	blood:	n/a	n/a
50	CTCF	chr2:47168100-47168250	HCFaa	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47166662..47168239-chr2:47214409..47216366,2	MCF-7	breast:
2	chr17:62502600..62503535-chr2:47167830..47168748,2	Hela-S3	cervix:
3	chr2:47167461..47169104-chr2:47203278..47205346,2	MCF-7	breast:
4	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
5	chr2:47166648..47168601-chr2:47272959..47275479,2	MCF-7	breast:
6	chr2:47166510..47168193-chr2:47197498..47199709,2	MCF-7	breast:
7	chr2:47166485..47169114-chr2:47402596..47405123,4	MCF-7	breast:
8	chr2:46768715..46770395-chr2:47165746..47168568,2	MCF-7	breast:
9	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
10	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
11	chr12:1100265..1100782-chr2:47168046..47168566,2	MCF-7	breast:
12	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
13	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
14	chr2:47167753..47168313-chr21:38738139..38738678,2	Hela-S3	cervix:
15	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
16	chr2:47167291..47170086-chr2:47204793..47207048,4	MCF-7	breast:
17	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
18	chr12:1100048..1100689-chr2:47168066..47168566,2	HCT-116	colon:
19	chr2:47167989..47168719-chr20:43514228..43514841,2	Hela-S3	cervix:
20	chr2:47141557..47143529-chr2:47167839..47169788,2	K562	blood:
21	chr2:47141053..47143152-chr2:47167792..47169429,2	MCF-7	breast:
22	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000166913	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000250132	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000273210	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000082805	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv3427405	chr2:47166973-47169821	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
7	esv3332265	chr2:47167448-47169546	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	14 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	chr2:47167000-47168200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr2:47167200-47168200	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr2:47167200-47168200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr2:47167200-47168200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr2:47167200-47168200	Flanking Active TSS	Colonic Mucosa	Colon
6	chr2:47167400-47169000	Active TSS	Right Atrium	heart
7	chr2:47167400-47169200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:47167400-47169400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:47167400-47169600	Active TSS	H9 Cell Line	embryonic stem cell
10	chr2:47167600-47168200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
11	chr2:47167600-47168200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr2:47167600-47168200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:47167600-47168200	Flanking Active TSS	Dnd41	blood
14	chr2:47167600-47168800	Active TSS	Fetal Brain Female	brain
15	chr2:47167600-47169000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:47167600-47169000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:47167600-47169000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr2:47167600-47169000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:47167600-47169000	Active TSS	Psoas Muscle	Psoas
20	chr2:47167600-47169200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:47167600-47169200	Active TSS	Brain Substantia Nigra	brain
22	chr2:47167600-47169400	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr2:47167600-47169400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:47167600-47169600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:47167600-47169600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:47167600-47169600	Active TSS	Primary T cells from cord blood	blood
27	chr2:47167600-47169600	Active TSS	Right Ventricle	heart
28	chr2:47167600-47169800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr2:47167600-47169800	Active TSS	Fetal Kidney	kidney
30	chr2:47167600-47169800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:47167600-47170000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:47167600-47170400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:47167600-47170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr2:47167600-47170400	Active TSS	Rectal Smooth Muscle	rectum
35	chr2:47167600-47170600	Active TSS	Thymus	Thymus
36	chr2:47167800-47168600	Active TSS	Stomach Smooth Muscle	stomach
37	chr2:47167800-47168600	Active TSS	HepG2	liver
38	chr2:47167800-47168800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr2:47167800-47168800	Weak transcription	Fetal Brain Male	brain
40	chr2:47167800-47168800	Active TSS	Fetal Stomach	stomach
41	chr2:47167800-47169000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr2:47167800-47169000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:47167800-47169000	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr2:47167800-47169000	Active TSS	iPS-20b Cell Line	embryonic stem cell
45	chr2:47167800-47169000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:47167800-47169000	Active TSS	Duodenum Mucosa	Duodenum
47	chr2:47167800-47169000	Active TSS	Fetal Intestine Large	intestine
48	chr2:47167800-47169000	Active TSS	Fetal Intestine Small	intestine
49	chr2:47167800-47169000	Active TSS	Fetal Lung	lung
50	chr2:47167800-47169000	Active TSS	HSMMtube	muscle

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