Variant report

Variant	rs2388991
Chromosome Location	chr12:32630801-32630802
allele	G/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	POLR2A	chr12:32630619-32631018	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr12:32630605-32630954	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr12:32630700-32630850	BE2_C	brain:	n/a	n/a
4	EP300	chr12:32630586-32631079	SK-N-SH_RA	brain:	n/a	chr12:32630632-32630645
5	TCF12	chr12:32630540-32631119	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr12:32630369-32631229	SK-N-SH	brain:	n/a	n/a
7	RAD21	chr12:32630684-32630925	SK-N-SH_RA	brain:	n/a	n/a
8	FOXP2	chr12:32630695-32630938	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:32630789-32630939	H1-hESC	embryonic stem cell:	n/a	n/a
10	EP300	chr12:32630597-32631088	SK-N-SH_RA	brain:	n/a	chr12:32630632-32630645 chr12:32631070-32631084

Variant related genes	Relation type
RNU6-494P	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11052012	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11052014	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052015	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367135	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs1566513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047643	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs34382604	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34957239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61927222	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32602600-32636400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:32610800-32636400	Weak transcription	NHEK	skin
4	chr12:32610800-32639000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr12:32616000-32638600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:32619600-32642000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:32621600-32631200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr12:32621600-32636400	Weak transcription	Right Ventricle	heart
9	chr12:32621800-32631200	Weak transcription	HUVEC	blood vessel
10	chr12:32621800-32654000	Weak transcription	Lung	lung
11	chr12:32622000-32631200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr12:32624800-32636400	Weak transcription	HMEC	breast
13	chr12:32625000-32631200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:32625000-32631200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr12:32625000-32631600	Weak transcription	Liver	Liver
16	chr12:32625000-32636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:32625000-32655800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:32625200-32636400	Weak transcription	Gastric	stomach
19	chr12:32625200-32655200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:32627200-32638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:32627600-32631200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:32628200-32632000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:32628600-32633000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr12:32628600-32637200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr12:32629400-32643600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:32629600-32632000	Enhancers	HSMM	muscle
27	chr12:32629600-32635400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:32629600-32643000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:32629800-32631200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr12:32629800-32631200	Weak transcription	Fetal Intestine Large	intestine
31	chr12:32629800-32631600	Weak transcription	Stomach Mucosa	stomach
32	chr12:32629800-32632800	Weak transcription	Pancreas	Pancrea
33	chr12:32629800-32633800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr12:32629800-32634200	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr12:32629800-32634400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:32629800-32634800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:32629800-32636000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:32629800-32636400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:32629800-32636400	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:32629800-32636400	Weak transcription	Left Ventricle	heart
41	chr12:32630000-32634800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr12:32630000-32638800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:32630200-32631600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:32630400-32631000	Enhancers	Brain Germinal Matrix	brain
45	chr12:32630400-32631000	Enhancers	Fetal Kidney	kidney
46	chr12:32630400-32631600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:32630400-32631800	Enhancers	Primary B cells from cord blood	blood
48	chr12:32630400-32632400	Enhancers	Primary B cells from peripheral blood	blood
49	chr12:32630600-32631400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:32630600-32631600	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links