Variant report

Variant	rs16862197
Chromosome Location	chr1:169430074-169430075
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	E2F6	chr1:169429466-169430108	H1-hESC	embryonic stem cell:	n/a	chr1:169429714-169429724 chr1:169429713-169429722
2	POLR2A	chr1:169429836-169432222	K562	blood:	n/a	n/a
3	MAX	chr1:169429526-169430170	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:169429641-169430085	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:169429729-169430092	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:169429397-169431229	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:169429705-169430196	HepG2	liver:	n/a	n/a
8	POLR2A	chr1:169429784-169430117	ProgFib	skin:	n/a	n/a
9	POLR2A	chr1:169429461-169430289	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:169429519-169430114	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000234437	TF binding region
CCDC181	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10919142	1.00[EUR][1000 genomes]
rs10919161	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10919171	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12068499	1.00[EUR][1000 genomes]
rs12071302	1.00[EUR][1000 genomes]
rs12073238	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12078569	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12081893	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12083695	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12088527	1.00[EUR][1000 genomes]
rs12088713	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12091844	0.92[YRI][hapmap]
rs12095660	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16862184	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3737683	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1005941	chr1:169410486-169456393	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169429200-169430200	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr1:169429200-169430400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:169429200-169430400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:169429400-169430200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr1:169429400-169430200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:169429400-169430200	Flanking Active TSS	Liver	Liver
7	chr1:169429400-169430200	Enhancers	Lung	lung
8	chr1:169429600-169430200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:169429600-169430200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
10	chr1:169429600-169430200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:169429600-169430200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:169429600-169430200	Enhancers	Esophagus	oesophagus
13	chr1:169429600-169430200	Bivalent Enhancer	Fetal Muscle Leg	muscle
14	chr1:169429600-169430200	Enhancers	Gastric	stomach
15	chr1:169429600-169430200	Enhancers	Pancreas	Pancrea
16	chr1:169429600-169430400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:169429600-169434600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:169429600-169448200	Weak transcription	Fetal Heart	heart
19	chr1:169429800-169430200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:169429800-169430200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:169429800-169430200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:169429800-169430200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:169429800-169430200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr1:169429800-169430200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr1:169429800-169430200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:169429800-169430200	Bivalent Enhancer	Aorta	Aorta
27	chr1:169429800-169430200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr1:169429800-169430200	Enhancers	Stomach Mucosa	stomach
29	chr1:169429800-169434400	Weak transcription	Placenta	Placenta
30	chr1:169429800-169436200	Weak transcription	Psoas Muscle	Psoas
31	chr1:169429800-169436200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:169429800-169436800	Weak transcription	Right Ventricle	heart
33	chr1:169429800-169446400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:169430000-169430200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:169430000-169430200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:169430000-169430200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:169430000-169430200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:169430000-169430200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:169430000-169430200	Enhancers	Adipose Nuclei	Adipose
40	chr1:169430000-169430200	Bivalent Enhancer	Colon Smooth Muscle	Colon
41	chr1:169430000-169430200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
42	chr1:169430000-169430200	Bivalent Enhancer	Fetal Brain Female	brain
43	chr1:169430000-169430200	Bivalent Enhancer	Fetal Lung	lung
44	chr1:169430000-169430200	Bivalent Enhancer	Fetal Stomach	stomach
45	chr1:169430000-169430200	Enhancers	Ovary	ovary
46	chr1:169430000-169430200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr1:169430000-169430200	Active TSS	Stomach Smooth Muscle	stomach
48	chr1:169430000-169430200	Enhancers	Thymus	Thymus
49	chr1:169430000-169430200	Active TSS	HepG2	liver
50	chr1:169430000-169430200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood

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