Variant report

Variant	rs7974099
Chromosome Location	chr12:123771475-123771476
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:123771276-123771790	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:123771173-123774237	K562	blood:	n/a	n/a
3	POLR2A	chr12:123771300-123771986	MCF-7	breast:	n/a	n/a
4	POLR2A	chr12:123771312-123771567	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:123771137-123772139	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr12:123771403-123771792	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:123771306-123771624	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr12:123771295-123771554	HCT-116	colon:	n/a	n/a
9	BCL3	chr12:123771233-123771663	A549	lung:	n/a	n/a
10	POLR2A	chr12:123771311-123771667	U87	brain:	n/a	n/a
11	POLR2A	chr12:123771378-123772064	K562	blood:	n/a	n/a
12	POLR2A	chr12:123771374-123771830	HepG2	liver:	n/a	n/a
13	POLR2A	chr12:123771341-123772036	A549	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:123769740..123772469-chr12:123873331..123875803,2	MCF-7	breast:
2	chr12:123754953..123756587-chr12:123771355..123773194,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP375	TF binding region
ENSG00000183955	Chromatin interaction
ENSG00000111328	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10082867	0.88[ASN][1000 genomes]
rs10444439	0.84[ASN][1000 genomes]
rs10444449	0.80[ASN][1000 genomes]
rs10773003	0.89[ASN][1000 genomes]
rs10773004	0.88[ASN][1000 genomes]
rs10773005	0.88[ASN][1000 genomes]
rs10773006	0.88[ASN][1000 genomes]
rs10846505	0.85[ASN][1000 genomes]
rs10846506	0.90[ASN][1000 genomes]
rs11057238	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11057242	0.91[ASN][1000 genomes]
rs11057248	0.87[ASN][1000 genomes]
rs11057251	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057254	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057261	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11057273	0.88[ASN][1000 genomes]
rs11057275	0.85[ASN][1000 genomes]
rs11057276	0.88[ASN][1000 genomes]
rs11057284	0.88[ASN][1000 genomes]
rs11503021	0.84[ASN][1000 genomes]
rs11608297	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11608305	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11611141	0.88[ASN][1000 genomes]
rs11611677	0.89[ASN][1000 genomes]
rs11611679	0.87[ASN][1000 genomes]
rs11611680	0.87[ASN][1000 genomes]
rs11611694	0.88[ASN][1000 genomes]
rs12317103	0.88[ASN][1000 genomes]
rs12317452	0.88[ASN][1000 genomes]
rs12366872	0.88[ASN][1000 genomes]
rs12367421	0.90[ASN][1000 genomes]
rs12582153	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13303208	0.83[ASN][1000 genomes]
rs28410096	0.87[ASN][1000 genomes]
rs28419092	0.88[ASN][1000 genomes]
rs28450974	0.87[ASN][1000 genomes]
rs28461471	0.87[ASN][1000 genomes]
rs28496545	0.81[ASN][1000 genomes]
rs28498205	0.87[ASN][1000 genomes]
rs28503862	0.87[ASN][1000 genomes]
rs28516750	0.83[ASN][1000 genomes]
rs28532037	0.87[ASN][1000 genomes]
rs28533432	0.87[ASN][1000 genomes]
rs28556815	0.81[ASN][1000 genomes]
rs28565984	0.83[ASN][1000 genomes]
rs28577594	0.81[ASN][1000 genomes]
rs28581850	0.87[ASN][1000 genomes]
rs28592032	0.87[ASN][1000 genomes]
rs28631104	0.85[ASN][1000 genomes]
rs28642812	0.81[ASN][1000 genomes]
rs28786830	0.87[ASN][1000 genomes]
rs28820735	0.87[ASN][1000 genomes]
rs28825193	0.87[ASN][1000 genomes]
rs28866344	0.83[ASN][1000 genomes]
rs3088303	0.90[ASN][1000 genomes]
rs34032470	0.82[ASN][1000 genomes]
rs35818434	0.87[ASN][1000 genomes]
rs4759375	0.87[ASN][1000 genomes]
rs4759377	0.88[ASN][1000 genomes]
rs56116847	0.87[ASN][1000 genomes]
rs60835840	0.87[ASN][1000 genomes]
rs61388686	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61953412	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6488873	0.82[ASN][1000 genomes]
rs7298909	0.88[ASN][1000 genomes]
rs7303754	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7312145	0.88[ASN][1000 genomes]
rs7315453	0.88[ASN][1000 genomes]
rs73216931	0.82[ASN][1000 genomes]
rs73231950	0.90[ASN][1000 genomes]
rs7954704	0.88[ASN][1000 genomes]
rs7972811	0.88[ASN][1000 genomes]
rs9669273	0.88[ASN][1000 genomes]
rs9669295	0.87[ASN][1000 genomes]
rs9705407	0.84[ASN][1000 genomes]
rs9739171	0.88[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	esv1825473	chr12:123582855-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv1803368	chr12:123640853-123822503	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	esv1830566	chr12:123640853-123822503	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	esv1836043	chr12:123709409-123822503	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv1038841	chr12:123757305-124087671	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription 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 miRNA target site	63 gene(s)	inside rSNPs	diseases
6	nsv541622	chr12:123757305-124087671	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7974099	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs7974099	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs7974099	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs7974099	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs7974099	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs7974099	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs7974099	CDK2AP1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123757200-123773800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr12:123757200-123774000	Weak transcription	K562	blood
3	chr12:123757200-123782600	Weak transcription	Right Atrium	heart
4	chr12:123757600-123773400	Weak transcription	Fetal Muscle Leg	muscle
5	chr12:123757600-123773400	Weak transcription	Fetal Thymus	thymus
6	chr12:123757600-123773800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr12:123758000-123771600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:123758000-123773400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:123758800-123773400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:123762800-123773400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:123763000-123773800	Weak transcription	Adipose Nuclei	Adipose
12	chr12:123763200-123772800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:123763200-123774000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:123763200-123775800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123763400-123773200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:123763400-123773400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:123763400-123774000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:123763400-123774600	Weak transcription	Primary B cells from cord blood	blood
19	chr12:123763400-123774600	Weak transcription	HUVEC	blood vessel
20	chr12:123763600-123773200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:123763600-123773400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:123763600-123773400	Weak transcription	GM12878-XiMat	blood
23	chr12:123763600-123774600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr12:123763800-123773800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr12:123766000-123771600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:123766200-123780000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr12:123767000-123773400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:123768400-123773000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr12:123768800-123772200	Weak transcription	Fetal Intestine Small	intestine
30	chr12:123769600-123772400	Weak transcription	Fetal Stomach	stomach
31	chr12:123769600-123773800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:123769600-123775000	Weak transcription	HepG2	liver
33	chr12:123769800-123778800	Weak transcription	Fetal Kidney	kidney
34	chr12:123770000-123772200	Enhancers	Fetal Brain Male	brain
35	chr12:123770000-123772400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:123770200-123776800	Weak transcription	Spleen	Spleen
37	chr12:123770200-123778400	Weak transcription	Fetal Lung	lung
38	chr12:123770600-123773200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:123770800-123771600	Weak transcription	NH-A	brain
40	chr12:123771000-123773400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:123771200-123771600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr12:123771200-123771800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr12:123771200-123772000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:123771200-123772000	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr12:123771200-123772000	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr12:123771200-123772000	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr12:123771200-123772000	Enhancers	Fetal Brain Female	brain
48	chr12:123771200-123773200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:123771200-123773200	Weak transcription	Primary T cells from cord blood	blood
50	chr12:123771200-123773200	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links