Variant report

Variant	rs549400710
Chromosome Location	chr2:47168636-47168637
allele	A/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	RAD21	chr2:47168551-47169370	A549	lung:	n/a	n/a
2	HEY1	chr2:47168610-47169265	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:47167999-47168637	PANC-1	pancreas:	n/a	n/a
4	CTCF	chr2:47168600-47168750	HepG2	liver:	n/a	n/a
5	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
6	POLR2A	chr2:47168048-47169610	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:47168038-47169209	K562	blood:	n/a	n/a
8	TCF3	chr2:47168108-47169060	GM12878	blood:	n/a	n/a
9	POLR2A	chr2:47168245-47169855	GM12892	blood:	n/a	n/a
10	MAX	chr2:47168564-47169187	SK-N-SH	brain:	n/a	chr2:47169037-47169048
11	REST	chr2:47168602-47168882	A549	lung:	n/a	n/a
12	TAF1	chr2:47168110-47169018	HepG2	liver:	n/a	n/a
13	CREB1	chr2:47167831-47169080	A549	lung:	n/a	chr2:47168009-47168022
14	E2F6	chr2:47168563-47169108	K562	blood:	n/a	chr2:47168901-47168909 chr2:47168958-47168968
15	ZBTB7A	chr2:47167467-47169239	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr2:47167996-47169186	K562	blood:	n/a	n/a
17	POLR2A	chr2:47167706-47169478	HUVEC	blood vessel:	n/a	n/a
18	YY1	chr2:47168081-47169510	GM12892	blood:	n/a	chr2:47168670-47168690 chr2:47168245-47168259 chr2:47168676-47168688
19	MAX	chr2:47167603-47169355	K562	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
20	MAX	chr2:47168615-47169131	A549	lung:	n/a	chr2:47169037-47169048
21	POLR2A	chr2:47167805-47169022	A549	lung:	n/a	n/a
22	RUNX3	chr2:47168562-47169995	GM12878	blood:	n/a	chr2:47169041-47169056
23	MYC	chr2:47167697-47169785	NB4	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
24	CHD2	chr2:47168605-47169105	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr2:47168032-47169485	MCF-7	breast:	n/a	n/a
26	YY1	chr2:47168548-47168981	GM12891	blood:	n/a	chr2:47168670-47168690 chr2:47168676-47168688
27	MXI1	chr2:47166976-47169461	HepG2	liver:	n/a	n/a
28	GATA3	chr2:47167309-47169655	A549	lung:	n/a	chr2:47169431-47169439
29	ELF1	chr2:47168142-47169118	GM12878	blood:	n/a	chr2:47168240-47168252
30	POLR2A	chr2:47168634-47169056	HepG2	liver:	n/a	n/a
31	MAX	chr2:47167779-47169115	HepG2	liver:	n/a	chr2:47168106-47168116 chr2:47169037-47169048
32	POLR2A	chr2:47168180-47169840	GM12878	blood:	n/a	n/a
33	YY1	chr2:47167765-47169076	HepG2	liver:	n/a	chr2:47168670-47168690 chr2:47168245-47168259 chr2:47167942-47167953 chr2:47168676-47168688
34	MAX	chr2:47167138-47169869	Hela-S3	cervix:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
35	TAF1	chr2:47168611-47168855	GM12891	blood:	n/a	n/a
36	IRF1	chr2:47168170-47169177	K562	blood:	n/a	chr2:47169061-47169070
37	TAF1	chr2:47168556-47169447	A549	lung:	n/a	n/a
38	MYC	chr2:47168198-47169055	MCF10A-Er-Src	breast:	n/a	chr2:47169037-47169048
39	SMARCB1	chr2:47167445-47169505	Hela-S3	cervix:	n/a	n/a
40	MAX	chr2:47168271-47169627	NB4	blood:	n/a	chr2:47169037-47169048
41	RCOR1	chr2:47168573-47169909	GM12878	blood:	n/a	n/a
42	MYC	chr2:47167712-47169673	K562	blood:	n/a	chr2:47168106-47168116 chr2:47169037-47169048 chr2:47167751-47167760
43	POLR2A	chr2:47166646-47169549	HepG2	liver:	n/a	n/a
44	POLR2A	chr2:47168578-47169659	GM12891	blood:	n/a	n/a
45	POLR2A	chr2:47167963-47169919	GM12892	blood:	n/a	n/a
46	SP1	chr2:47168594-47169142	A549	lung:	n/a	n/a
47	POLR2A	chr2:47167989-47169640	GM10847	blood:	n/a	n/a
48	POLR2A	chr2:47168548-47169305	U87	brain:	n/a	n/a
49	POLR2A	chr2:47168542-47169385	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:47168589-47169185	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:62502600..62503535-chr2:47167830..47168748,2	Hela-S3	cervix:
2	chr2:47167461..47169104-chr2:47203278..47205346,2	MCF-7	breast:
3	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
4	chr2:47166485..47169114-chr2:47402596..47405123,4	MCF-7	breast:
5	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
6	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
7	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
8	chr2:47165446..47170208-chr2:47173646..47177856,9	MCF-7	breast:
9	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
10	chr2:47167291..47170086-chr2:47204793..47207048,4	MCF-7	breast:
11	chr18:29598516..29599058-chr2:47168202..47168759,2	Hela-S3	cervix:
12	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
13	chr2:47168340..47172583-chr2:47183123..47189203,6	MCF-7	breast:
14	chr2:47167989..47168719-chr20:43514228..43514841,2	Hela-S3	cervix:
15	chr2:47141557..47143529-chr2:47167839..47169788,2	K562	blood:
16	chr2:47141053..47143152-chr2:47167792..47169429,2	MCF-7	breast:
17	chr2:47166107..47171055-chr2:47402078..47404965,9	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000166913	Chromatin interaction
ENSG00000263917	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000272814	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000180398	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	chr2:47167400-47169000	Active TSS	Right Atrium	heart
2	chr2:47167400-47169200	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:47167400-47169400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:47167400-47169600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:47167600-47168800	Active TSS	Fetal Brain Female	brain
6	chr2:47167600-47169000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:47167600-47169000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:47167600-47169000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr2:47167600-47169000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:47167600-47169000	Active TSS	Psoas Muscle	Psoas
11	chr2:47167600-47169200	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr2:47167600-47169200	Active TSS	Brain Substantia Nigra	brain
13	chr2:47167600-47169400	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:47167600-47169400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:47167600-47169600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:47167600-47169600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:47167600-47169600	Active TSS	Primary T cells from cord blood	blood
18	chr2:47167600-47169600	Active TSS	Right Ventricle	heart
19	chr2:47167600-47169800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr2:47167600-47169800	Active TSS	Fetal Kidney	kidney
21	chr2:47167600-47169800	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:47167600-47170000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:47167600-47170400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:47167600-47170400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:47167600-47170400	Active TSS	Rectal Smooth Muscle	rectum
26	chr2:47167600-47170600	Active TSS	Thymus	Thymus
27	chr2:47167800-47168800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:47167800-47168800	Weak transcription	Fetal Brain Male	brain
29	chr2:47167800-47168800	Active TSS	Fetal Stomach	stomach
30	chr2:47167800-47169000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:47167800-47169000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr2:47167800-47169000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr2:47167800-47169000	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr2:47167800-47169000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:47167800-47169000	Active TSS	Duodenum Mucosa	Duodenum
36	chr2:47167800-47169000	Active TSS	Fetal Intestine Large	intestine
37	chr2:47167800-47169000	Active TSS	Fetal Intestine Small	intestine
38	chr2:47167800-47169000	Active TSS	Fetal Lung	lung
39	chr2:47167800-47169000	Active TSS	HSMMtube	muscle
40	chr2:47167800-47169000	Active TSS	K562	blood
41	chr2:47167800-47169200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:47167800-47169200	Active TSS	Primary B cells from peripheral blood	blood
43	chr2:47167800-47169200	Active TSS	Brain Angular Gyrus	brain
44	chr2:47167800-47169200	Active TSS	Brain Anterior Caudate	brain
45	chr2:47167800-47169200	Active TSS	Brain Cingulate Gyrus	brain
46	chr2:47167800-47169200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:47167800-47169200	Active TSS	Colon Smooth Muscle	Colon
48	chr2:47167800-47169200	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:47167800-47169400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:47167800-47169400	Active TSS	iPS-15b Cell Line	embryonic stem cell

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