Variant report

Variant	rs12098435
Chromosome Location	chr10:91090488-91090489
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	PBX3	chr10:91090384-91090657	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr10:91090143-91090872	SK-N-SH	brain:	n/a	chr10:91090552-91090563
3	TCF12	chr10:91090175-91090825	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr10:91090313-91090812	SK-N-SH	brain:	n/a	chr10:91090552-91090563
5	EP300	chr10:91090366-91090723	SK-N-SH_RA	brain:	n/a	chr10:91090377-91090386
6	POLR2A	chr10:91089798-91091263	GM12891	blood:	n/a	n/a
7	EP300	chr10:91090345-91090707	SK-N-SH_RA	brain:	n/a	chr10:91090377-91090386
8	POLR2A	chr10:91089877-91091493	GM19099	blood:	n/a	n/a

Variant related genes	Relation type
IFIT3	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10887966	1.00[EUR][1000 genomes]
rs10887967	1.00[EUR][1000 genomes]
rs10887968	1.00[EUR][1000 genomes]
rs11185731	1.00[EUR][1000 genomes]
rs11185734	1.00[EUR][1000 genomes]
rs11185736	1.00[EUR][1000 genomes]
rs11203078	0.80[YRI][hapmap]
rs11203141	1.00[EUR][1000 genomes]
rs11813257	1.00[EUR][1000 genomes]
rs12098668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34407818	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs41284952	1.00[EUR][1000 genomes]
rs57529139	1.00[EUR][1000 genomes]
rs57947325	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7077187	0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7077376	1.00[EUR][1000 genomes]
rs7080667	1.00[EUR][1000 genomes]
rs7101353	1.00[EUR][1000 genomes]
rs73368509	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73371311	1.00[EUR][1000 genomes]
rs7342121	1.00[EUR][1000 genomes]
rs74146910	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7476546	1.00[EUR][1000 genomes]
rs7922613	0.89[AMR][1000 genomes]
rs812451	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv1041964	chr10:90861380-91378356	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv1040375	chr10:91022218-91153074	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv34085	chr10:91065949-91174175	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91087200-91093600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:91088000-91091000	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr10:91088000-91091200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr10:91088000-91099800	Weak transcription	Gastric	stomach
5	chr10:91088200-91090600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr10:91088200-91090600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr10:91088200-91090600	Weak transcription	Stomach Mucosa	stomach
8	chr10:91088200-91091800	Enhancers	Primary B cells from peripheral blood	blood
9	chr10:91088200-91091800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr10:91088200-91092000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:91088200-91092000	Weak transcription	Aorta	Aorta
12	chr10:91088200-91092400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr10:91088200-91093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr10:91088200-91093400	Weak transcription	Esophagus	oesophagus
15	chr10:91088400-91090800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr10:91088400-91091000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr10:91088400-91091800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:91088400-91091800	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr10:91088400-91091800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr10:91088400-91092000	Enhancers	Fetal Intestine Large	intestine
21	chr10:91088400-91092200	Weak transcription	HMEC	breast
22	chr10:91088600-91090800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr10:91088600-91091200	Weak transcription	Fetal Brain Male	brain
24	chr10:91088600-91091600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr10:91088600-91091800	Weak transcription	K562	blood
26	chr10:91088600-91092200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr10:91088800-91090600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr10:91088800-91091400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:91088800-91091400	Weak transcription	Primary B cells from cord blood	blood
30	chr10:91088800-91091800	Enhancers	Dnd41	blood
31	chr10:91088800-91092000	Weak transcription	A549	lung
32	chr10:91088800-91092200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr10:91088800-91092200	Enhancers	Left Ventricle	heart
34	chr10:91088800-91092600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:91089000-91091200	Enhancers	Colon Smooth Muscle	Colon
36	chr10:91089000-91091800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:91089000-91091800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr10:91089000-91091800	Enhancers	Fetal Intestine Small	intestine
39	chr10:91089000-91091800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr10:91089000-91091800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr10:91089000-91091800	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:91089000-91091800	Weak transcription	HSMMtube	muscle
43	chr10:91089000-91091800	Enhancers	NHDF-Ad	bronchial
44	chr10:91089000-91092000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr10:91089000-91092000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr10:91089000-91092000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr10:91089000-91092200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr10:91089000-91092200	Weak transcription	Fetal Heart	heart
49	chr10:91089200-91090600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr10:91089200-91090800	Enhancers	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links