Variant report

Variant	rs12028854
Chromosome Location	chr1:150487636-150487637
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	TBP	chr1:150487588-150488555	K562	blood:	n/a	n/a
2	POLR2A	chr1:150487595-150488533	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:150487631-150488525	HUVEC	blood vessel:	n/a	n/a
4	KAP1	chr1:150487587-150488329	U2OS	brain:	n/a	n/a
5	EBF1	chr1:150487579-150487983	GM12878	blood:	n/a	chr1:150487794-150487804 chr1:150487794-150487803 chr1:150487793-150487804
6	TCF7L2	chr1:150487079-150488431	HEK293	kidney:	n/a	chr1:150487621-150487630
7	TCF7L2	chr1:150487534-150488420	MCF-7	breast:	n/a	chr1:150487621-150487630
8	PBX3	chr1:150487574-150488541	SK-N-SH	brain:	n/a	chr1:150488090-150488099 chr1:150488073-150488082
9	TCF7L2	chr1:150487493-150488435	Hela-S3	cervix:	n/a	chr1:150487621-150487630
10	TAF1	chr1:150487570-150488430	MCF-7	breast:	n/a	n/a
11	E2F6	chr1:150487618-150488475	K562	blood:	n/a	chr1:150488214-150488223
12	POLR2A	chr1:150487560-150488653	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr1:150487558-150488475	K562	blood:	n/a	n/a
14	MYC	chr1:150487628-150489424	K562	blood:	n/a	chr1:150488736-150488746
15	MXI1	chr1:150487303-150489576	SK-N-SH	brain:	n/a	chr1:150488069-150488078
16	JUND	chr1:150487600-150488262	H1-hESC	embryonic stem cell:	n/a	chr1:150488091-150488100
17	UBTF	chr1:150487491-150488453	K562	blood:	n/a	n/a
18	POLR2A	chr1:150487431-150488501	U87	brain:	n/a	n/a
19	NR2F2	chr1:150487295-150488581	K562	blood:	n/a	n/a
20	POLR2A	chr1:150487575-150488432	HepG2	liver:	n/a	n/a
21	POLR2A	chr1:150487618-150488467	K562	blood:	n/a	n/a
22	SMARCB1	chr1:150487599-150488502	Hela-S3	cervix:	n/a	n/a
23	TEAD4	chr1:150487475-150488114	K562	blood:	n/a	n/a
24	TCF12	chr1:150487467-150488553	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr1:150487567-150488491	ProgFib	skin:	n/a	n/a
26	MXI1	chr1:150487538-150488455	HepG2	liver:	n/a	chr1:150488069-150488078
27	CBX3	chr1:150487584-150488570	K562	blood:	n/a	n/a
28	SIN3A	chr1:150487608-150488427	H1-hESC	embryonic stem cell:	n/a	chr1:150487655-150487663
29	POLR2A	chr1:150487583-150488042	HepG2	liver:	n/a	n/a
30	JUN	chr1:150486955-150488530	K562	blood:	n/a	chr1:150488091-150488100
31	CREB1	chr1:150487552-150488522	A549	lung:	n/a	n/a
32	MTA3	chr1:150487466-150488422	GM12878	blood:	n/a	n/a
33	TCF7L2	chr1:150487420-150488461	PANC-1	pancreas:	n/a	chr1:150487621-150487630
34	HEY1	chr1:150487507-150488437	HepG2	liver:	n/a	chr1:150488109-150488124
35	STAT5A	chr1:150487473-150488410	GM12878	blood:	n/a	n/a
36	MAX	chr1:150487455-150488516	HepG2	liver:	n/a	n/a
37	POLR2A	chr1:150487631-150488513	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:150487569-150487727	H1-hESC	embryonic stem cell:	n/a	n/a
39	PBX3	chr1:150487585-150488469	SK-N-SH	brain:	n/a	chr1:150488090-150488099 chr1:150488073-150488082
40	MBD4	chr1:150487492-150488044	HepG2	liver:	n/a	n/a
41	REST	chr1:150487612-150489055	H1-neurons	neurons:	n/a	chr1:150488111-150488118
42	POLR2A	chr1:150487590-150488460	U87	brain:	n/a	n/a
43	MAX	chr1:150487536-150488541	A549	lung:	n/a	n/a
44	TCF7L2	chr1:150487574-150488392	Hela-S3	cervix:	n/a	chr1:150487621-150487630
45	MAX	chr1:150487335-150488519	MCF-7	breast:	n/a	n/a
46	POLR2A	chr1:150486567-150488452	K562	blood:	n/a	n/a
47	NRF1	chr1:150487294-150488528	SK-N-SH	brain:	n/a	chr1:150488213-150488222 chr1:150488213-150488224 chr1:150488213-150488224 chr1:150488210-150488224
48	ZNF384	chr1:150487426-150488050	K562	blood:	n/a	n/a
49	MAZ	chr1:150487253-150488943	IMR90	lung:	n/a	chr1:150488736-150488746
50	EGR1	chr1:150487345-150488514	MCF-7	breast:	n/a	chr1:150488150-150488160

No.	Distal block	Cell Line	Cell type
1	chr1:150234614..150237282-chr1:150487610..150489545,2	K562	blood:
2	chr1:150486264..150488828-chr1:150527799..150530470,2	K562	blood:
3	chr1:150458274..150463765-chr1:150483214..150490747,8	K562	blood:
4	chr1:150458065..150461622-chr1:150486691..150490573,5	MCF-7	breast:
5	chr1:150486269..150489101-chr1:150530293..150532763,2	MCF-7	breast:
6	chr1:150487333..150489679-chr1:150520233..150523176,3	MCF-7	breast:
7	chr1:150458483..150461483-chr1:150486453..150489390,6	MCF-7	breast:
8	chr1:150485975..150488334-chr1:151205164..151207735,2	K562	blood:
9	chr1:150335902..150337829-chr1:150486316..150488661,2	MCF-7	breast:

Variant related genes	Relation type
LINC00568	TF binding region
ENSG00000118298	Chromatin interaction
ENSG00000225996	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000237781	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12039882	0.81[JPT][hapmap]
rs16836186	0.88[CHB][hapmap];0.80[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150486800-150487800	Flanking Active TSS	Colonic Mucosa	Colon
2	chr1:150486800-150487800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:150486800-150487800	Enhancers	Spleen	Spleen
4	chr1:150487000-150487800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:150487200-150488200	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr1:150487200-150488800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:150487200-150488800	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:150487200-150488800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:150487200-150489000	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:150487200-150489000	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:150487200-150489200	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr1:150487400-150487800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:150487400-150487800	Flanking Active TSS	Primary B cells from peripheral blood	blood
14	chr1:150487400-150487800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr1:150487400-150487800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:150487400-150487800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:150487400-150487800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:150487400-150487800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:150487400-150487800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:150487400-150487800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr1:150487400-150487800	Flanking Active TSS	Brain Germinal Matrix	brain
22	chr1:150487400-150487800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr1:150487400-150487800	Flanking Active TSS	Fetal Brain Female	brain
24	chr1:150487400-150487800	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr1:150487400-150487800	Flanking Active TSS	Fetal Intestine Small	intestine
26	chr1:150487400-150487800	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr1:150487400-150487800	Flanking Active TSS	GM12878-XiMat	blood
28	chr1:150487400-150488000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:150487400-150488000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr1:150487400-150488000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr1:150487400-150488000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr1:150487400-150488000	Flanking Active TSS	Liver	Liver
33	chr1:150487400-150488000	Flanking Active TSS	Duodenum Mucosa	Duodenum
34	chr1:150487400-150488000	Flanking Active TSS	Placenta	Placenta
35	chr1:150487400-150488000	Flanking Active TSS	Fetal Thymus	thymus
36	chr1:150487400-150488000	Flanking Active TSS	HMEC	breast
37	chr1:150487400-150488000	Flanking Active TSS	HSMMtube	muscle
38	chr1:150487400-150488000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr1:150487400-150488000	Flanking Active TSS	NHEK	skin
40	chr1:150487400-150488200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr1:150487400-150488200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:150487400-150488400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr1:150487400-150488600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr1:150487400-150488600	Active TSS	HUVEC	blood vessel
45	chr1:150487400-150488800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:150487400-150488800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:150487400-150488800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr1:150487400-150488800	Active TSS	iPS-18 Cell Line	embryonic stem cell
49	chr1:150487400-150488800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr1:150487400-150488800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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