Variant report

Variant	rs12057167
Chromosome Location	chr1:46123996-46123997
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	chr1:46123758-46124250	HepG2	liver:	n/a	chr1:46124020-46124027
2	POLR2A	chr1:46123959-46124051	K562	blood:	n/a	n/a
3	HNF4A	chr1:46123861-46124130	HepG2	liver:	n/a	chr1:46124018-46124033
4	HDAC2	chr1:46123847-46124148	HepG2	liver:	n/a	n/a
5	ARID3A	chr1:46123762-46124184	HepG2	liver:	n/a	n/a
6	NFIC	chr1:46123751-46124231	HepG2	liver:	n/a	n/a
7	FOXA2	chr1:46123547-46124452	HepG2	liver:	n/a	n/a
8	NR2F2	chr1:46123689-46124360	HepG2	liver:	n/a	n/a
9	BHLHE40	chr1:46123853-46124179	HepG2	liver:	n/a	n/a
10	RXRA	chr1:46123851-46124205	HepG2	liver:	n/a	n/a
11	HNF4G	chr1:46123718-46124141	HepG2	liver:	n/a	chr1:46124018-46124033
12	HNF4A	chr1:46123840-46124200	HepG2	liver:	n/a	chr1:46124018-46124033
13	HNF4A	chr1:46123743-46124141	HepG2	liver:	n/a	chr1:46124018-46124033
14	MYBL2	chr1:46123672-46124294	HepG2	liver:	n/a	n/a
15	HDAC2	chr1:46123745-46124227	HepG2	liver:	n/a	chr1:46124153-46124167 chr1:46124152-46124166 chr1:46124148-46124162 chr1:46124149-46124163
16	NFIC	chr1:46123801-46124188	HepG2	liver:	n/a	n/a
17	JUND	chr1:46123894-46124192	HepG2	liver:	n/a	n/a
18	NR2F2	chr1:46123682-46124334	HepG2	liver:	n/a	n/a
19	TEAD4	chr1:46123725-46124307	HepG2	liver:	n/a	n/a
20	FOXA1	chr1:46123845-46124126	HepG2	liver:	n/a	n/a
21	HNF4G	chr1:46123839-46124194	HepG2	liver:	n/a	chr1:46124018-46124033
22	FOXA1	chr1:46123697-46124136	HepG2	liver:	n/a	n/a
23	RAD21	chr1:46123759-46124165	HepG2	liver:	n/a	n/a
24	FOXA2	chr1:46123763-46124198	HepG2	liver:	n/a	n/a
25	RCOR1	chr1:46123885-46124094	HepG2	liver:	n/a	n/a
26	EP300	chr1:46123777-46124239	HepG2	liver:	n/a	chr1:46124153-46124167 chr1:46124159-46124173 chr1:46124151-46124165 chr1:46124096-46124103
27	EP300	chr1:46123718-46124188	HepG2	liver:	n/a	chr1:46124153-46124167 chr1:46124159-46124173 chr1:46124151-46124165 chr1:46124096-46124103
28	FOXA1	chr1:46123676-46124210	HepG2	liver:	n/a	n/a
29	TCF7L2	chr1:46123735-46124151	HepG2	liver:	n/a	n/a
30	MBD4	chr1:46123749-46124273	HepG2	liver:	n/a	n/a
31	FOXA1	chr1:46123701-46124274	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:46123763..46125674-chr1:46143555..46145505,2	K562	blood:
2	chr1:46122824..46126471-chr1:46150174..46153240,4	K562	blood:
3	chr1:46123716..46126422-chr1:46150615..46153415,2	MCF-7	breast:
4	chr1:46122824..46125811-chr1:46150999..46154065,3	K562	blood:
5	chr1:46098177..46100179-chr1:46123666..46125808,2	K562	blood:
6	chr1:46118216..46120545-chr1:46121839..46124168,2	K562	blood:

Variant related genes	Relation type
GPBP1L1	TF binding region
ENSG00000159596	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11211127	1.00[AMR][1000 genomes]
rs11211144	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211148	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211150	1.00[YRI][hapmap]
rs11211153	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211154	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211155	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211156	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12063380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064908	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12067882	1.00[AMR][1000 genomes]
rs12070146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070177	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073045	1.00[AMR][1000 genomes]
rs12073047	1.00[AMR][1000 genomes]
rs12073132	1.00[AMR][1000 genomes]
rs12077112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12081121	1.00[AMR][1000 genomes]
rs12082672	1.00[AMR][1000 genomes]
rs12085372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086880	1.00[AMR][1000 genomes]
rs12088810	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091335	1.00[AMR][1000 genomes]
rs12091360	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093444	1.00[AMR][1000 genomes]
rs12094011	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12097914	1.00[AMR][1000 genomes]
rs16832540	1.00[AMR][1000 genomes]
rs16832550	1.00[AMR][1000 genomes]
rs16832553	1.00[AMR][1000 genomes]
rs16832557	1.00[AMR][1000 genomes]
rs1691225	1.00[AMR][1000 genomes]
rs1691226	1.00[AMR][1000 genomes]
rs1691227	1.00[AMR][1000 genomes]
rs1762087	1.00[AMR][1000 genomes]
rs2782489	1.00[AMR][1000 genomes]
rs28532613	1.00[AMR][1000 genomes]
rs28548585	1.00[AMR][1000 genomes]
rs28576912	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28607905	1.00[AMR][1000 genomes]
rs35067820	1.00[AMR][1000 genomes]
rs35808563	1.00[AMR][1000 genomes]
rs486346	1.00[AMR][1000 genomes]
rs505175	1.00[AMR][1000 genomes]
rs506094	1.00[AMR][1000 genomes]
rs525706	1.00[AMR][1000 genomes]
rs622296	1.00[AMR][1000 genomes]
rs635446	1.00[AMR][1000 genomes]
rs665014	1.00[AMR][1000 genomes]
rs668289	1.00[AMR][1000 genomes]
rs6690210	1.00[YRI][hapmap]
rs669417	1.00[AMR][1000 genomes]
rs680267	1.00[AMR][1000 genomes]
rs7550744	1.00[AMR][1000 genomes]

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	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
2	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
4	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
5	nsv1011587	chr1:46051672-46244492	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv1014128	chr1:46097670-46394540	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 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	chr1:46053200-46127400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:46087600-46129200	Strong transcription	Fetal Thymus	thymus
3	chr1:46088600-46127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:46089600-46126400	Strong transcription	Primary T cells from cord blood	blood
5	chr1:46089800-46127000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:46091000-46126400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr1:46091200-46127000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:46091200-46127000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:46091200-46127200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:46091200-46128200	Strong transcription	Dnd41	blood
11	chr1:46091400-46127000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:46091400-46127000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:46091400-46127000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:46093200-46127000	Strong transcription	K562	blood
15	chr1:46097200-46126800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:46098400-46133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:46100200-46135600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:46106200-46140000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:46111400-46126200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:46111400-46126400	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:46111400-46126800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:46111600-46126000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:46112600-46126800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr1:46112600-46127000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:46112800-46126800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr1:46113000-46126600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:46113000-46126800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:46113000-46127000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr1:46113200-46127000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:46113200-46128000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:46113600-46124600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:46113600-46126000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr1:46113800-46126400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:46113800-46126800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:46113800-46127000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr1:46113800-46127000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:46113800-46127000	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:46113800-46127000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:46113800-46127000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr1:46113800-46133400	Weak transcription	Right Atrium	heart
41	chr1:46114000-46126600	Strong transcription	Placenta	Placenta
42	chr1:46114000-46127400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:46114000-46129200	Strong transcription	Primary B cells from cord blood	blood
44	chr1:46114200-46126400	Strong transcription	Adipose Nuclei	Adipose
45	chr1:46114200-46127000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:46114600-46126000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:46114600-46127600	Strong transcription	Hela-S3	cervix
48	chr1:46115400-46126400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:46115400-46126400	Strong transcription	Fetal Kidney	kidney
50	chr1:46115600-46127000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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