Variant report

Variant	rs7974732
Chromosome Location	chr12:120625512-120625513
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120624852..120626904-chr12:120728690..120730999,2	K562	blood:
2	chr12:120624823..120626354-chr12:120789006..120790806,2	MCF-7	breast:
3	chr12:120624216..120625857-chr12:120729184..120730823,2	MCF-7	breast:
4	chr12:120621069..120626352-chr12:120728235..120732450,5	K562	blood:
5	chr12:120611684..120613996-chr12:120624624..120626695,2	MCF-7	breast:
6	chr12:120619924..120622463-chr12:120623831..120626792,4	MCF-7	breast:
7	chr12:120619424..120625759-chr12:120727314..120731443,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200795	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11065036	0.90[ASN][1000 genomes]
rs11065040	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11833158	0.88[ASN][1000 genomes]
rs12305184	0.91[ASN][1000 genomes]
rs12306075	0.90[ASN][1000 genomes]
rs12310433	0.80[ASN][1000 genomes]
rs12320253	0.89[ASN][1000 genomes]
rs2074540	0.90[ASN][1000 genomes]
rs2240324	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2240325	0.90[ASN][1000 genomes]
rs2269945	0.89[ASN][1000 genomes]
rs2286050	0.90[ASN][1000 genomes]
rs2286051	0.90[ASN][1000 genomes]
rs3742039	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4522230	0.90[ASN][1000 genomes]
rs60271600	0.88[ASN][1000 genomes]
rs7133235	0.88[ASN][1000 genomes]
rs7134706	0.90[ASN][1000 genomes]
rs7135914	0.89[ASN][1000 genomes]
rs7296380	0.90[ASN][1000 genomes]
rs7299429	0.89[ASN][1000 genomes]
rs7310175	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7960120	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7978061	0.90[ASN][1000 genomes]
rs7978175	0.85[ASN][1000 genomes]
rs9630281	0.89[ASN][1000 genomes]
rs9651914	0.90[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	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	nsv899555	chr12:120519124-120840522	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	499 gene(s)	inside rSNPs	diseases
4	nsv519657	chr12:120533696-120676090	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
5	nsv560433	chr12:120533696-120676090	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	94 gene(s)	inside rSNPs	diseases
6	nsv832530	chr12:120586069-120758175	Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	484 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7974732	GCN1L1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120563000-120629800	Strong transcription	Fetal Stomach	stomach
2	chr12:120563000-120630200	Strong transcription	Fetal Muscle Leg	muscle
3	chr12:120563200-120630400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:120563400-120629200	Strong transcription	Fetal Intestine Small	intestine
5	chr12:120563400-120630200	Strong transcription	Fetal Thymus	thymus
6	chr12:120563600-120626000	Strong transcription	Brain Cingulate Gyrus	brain
7	chr12:120563600-120626200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr12:120563600-120629000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:120563600-120630200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr12:120563600-120630200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:120563600-120630200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr12:120563600-120630200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:120563600-120630200	Strong transcription	Fetal Muscle Trunk	muscle
14	chr12:120563800-120629800	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr12:120563800-120630000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr12:120563800-120630200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:120564200-120629600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:120564400-120628600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:120564400-120631800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr12:120565000-120628800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:120565000-120630200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:120565000-120630800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:120565200-120630200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:120565400-120628400	Strong transcription	Adipose Nuclei	Adipose
25	chr12:120565800-120629400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:120565800-120630200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:120565800-120630400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:120571200-120628200	Strong transcription	Fetal Intestine Large	intestine
29	chr12:120594200-120631600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:120594600-120630200	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr12:120601400-120628400	Strong transcription	Liver	Liver
32	chr12:120604600-120630200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:120604600-120630200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr12:120604800-120628200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:120605000-120628200	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:120605000-120628400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:120605000-120628400	Strong transcription	Brain Hippocampus Middle	brain
38	chr12:120605000-120628600	Strong transcription	Dnd41	blood
39	chr12:120605000-120630200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:120605200-120628200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr12:120605200-120628800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr12:120605200-120629800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr12:120605400-120627600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:120605400-120630200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:120605600-120627200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:120605600-120629400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr12:120605600-120629800	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr12:120605800-120629000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:120606200-120630200	Strong transcription	NHEK	skin
50	chr12:120606200-120630800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links