Variant report

Variant	rs28631104
Chromosome Location	chr12:123846812-123846813
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123749757..123758492-chr12:123844437..123851411,15	MCF-7	breast:
2	chr12:123844945..123846829-chr12:123847352..123848905,2	MCF-7	breast:
3	chr12:123846590..123852305-chr12:123861449..123873718,39	K562	blood:
4	chr12:123829057..123831002-chr12:123845125..123847852,2	K562	blood:
5	chr12:123845329..123854937-chr12:123865496..123876607,58	K562	blood:
6	chr12:123845591..123852236-chr12:123866929..123875043,19	MCF-7	breast:
7	chr12:123846000..123850093-chr12:124067189..124070124,4	K562	blood:
8	chr12:123844989..123847500-chr12:124065839..124068689,2	K562	blood:
9	chr12:123753451..123758032-chr12:123846651..123850459,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247373	Chromatin interaction
ENSG00000111328	Chromatin interaction
ENSG00000256092	Chromatin interaction
ENSG00000183955	Chromatin interaction
ENSG00000086598	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10082867	0.92[ASN][1000 genomes]
rs10444439	0.81[ASN][1000 genomes]
rs10773003	0.88[ASN][1000 genomes]
rs10773004	0.91[ASN][1000 genomes]
rs10773005	0.91[ASN][1000 genomes]
rs10773006	0.91[ASN][1000 genomes]
rs10773013	0.80[ASN][1000 genomes]
rs10846505	0.84[ASN][1000 genomes]
rs10846506	0.89[ASN][1000 genomes]
rs11057242	0.87[ASN][1000 genomes]
rs11057248	0.88[ASN][1000 genomes]
rs11057251	0.91[ASN][1000 genomes]
rs11057254	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057261	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057273	0.92[ASN][1000 genomes]
rs11057275	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11057276	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11057284	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11503021	0.91[ASN][1000 genomes]
rs11608297	0.93[ASN][1000 genomes]
rs11608305	0.91[ASN][1000 genomes]
rs11611141	0.92[ASN][1000 genomes]
rs11611677	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611679	0.92[ASN][1000 genomes]
rs11611680	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11611694	0.92[ASN][1000 genomes]
rs12317103	0.92[ASN][1000 genomes]
rs12317452	0.91[ASN][1000 genomes]
rs12366872	0.92[ASN][1000 genomes]
rs12367421	0.89[ASN][1000 genomes]
rs12582153	0.89[ASN][1000 genomes]
rs13303208	0.85[ASN][1000 genomes]
rs28410096	0.91[ASN][1000 genomes]
rs28419092	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28450974	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28461471	0.91[ASN][1000 genomes]
rs28496545	0.84[ASN][1000 genomes]
rs28498205	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28503862	0.91[ASN][1000 genomes]
rs28516750	0.87[ASN][1000 genomes]
rs28532037	0.91[ASN][1000 genomes]
rs28533432	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28556815	0.92[ASN][1000 genomes]
rs28565984	0.91[ASN][1000 genomes]
rs28574664	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28577594	0.85[ASN][1000 genomes]
rs28581850	0.91[ASN][1000 genomes]
rs28592032	0.91[ASN][1000 genomes]
rs28642812	0.85[ASN][1000 genomes]
rs28660993	0.83[ASN][1000 genomes]
rs28690326	0.80[ASN][1000 genomes]
rs28786830	0.91[ASN][1000 genomes]
rs28820735	0.91[ASN][1000 genomes]
rs28825193	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28866344	0.87[ASN][1000 genomes]
rs3088303	0.89[ASN][1000 genomes]
rs34032470	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35818434	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759375	0.91[ASN][1000 genomes]
rs4759377	0.92[ASN][1000 genomes]
rs56116847	0.91[ASN][1000 genomes]
rs56197170	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56309603	0.83[ASN][1000 genomes]
rs60835840	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61388686	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61955125	0.83[ASN][1000 genomes]
rs6416290	0.88[ASN][1000 genomes]
rs6488873	0.97[ASN][1000 genomes]
rs7298909	0.92[ASN][1000 genomes]
rs7312145	0.92[ASN][1000 genomes]
rs7315453	0.92[ASN][1000 genomes]
rs73216931	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73231950	0.89[ASN][1000 genomes]
rs7954704	0.92[ASN][1000 genomes]
rs7972811	0.92[ASN][1000 genomes]
rs7974099	0.85[ASN][1000 genomes]
rs9669273	0.92[ASN][1000 genomes]
rs9669295	0.91[ASN][1000 genomes]
rs9705407	0.88[ASN][1000 genomes]
rs9739171	0.92[ASN][1000 genomes]

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	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
2	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
3	nsv1035223	chr12:123795559-123991706	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv899579	chr12:123843017-123901480	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs28631104	LOC283378	Cis_1M	lymphoblastoid	RTeQTL
rs28631104	SBNO1	Cis_1M	lymphoblastoid	RTeQTL
rs28631104	MPHOSPH9	Cis_1M	lymphoblastoid	RTeQTL
rs28631104	ARL6IP4	Cis_1M	lymphoblastoid	RTeQTL
rs28631104	RP11-282O18.3	cis	Esophagus Mucosa	GTEx
rs28631104	CDK2AP1	Cis_1M	lymphoblastoid	RTeQTL
rs28631104	CDK2AP1	cis	Esophagus Mucosa	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123772400-123847800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:123816000-123847400	Weak transcription	Stomach Mucosa	stomach
3	chr12:123820400-123847000	Weak transcription	Fetal Brain Male	brain
4	chr12:123829000-123847400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:123830000-123847400	Weak transcription	Brain Substantia Nigra	brain
6	chr12:123830000-123847400	Weak transcription	Colonic Mucosa	Colon
7	chr12:123830000-123847400	Weak transcription	NHLF	lung
8	chr12:123830200-123847400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr12:123830200-123847400	Weak transcription	NHDF-Ad	bronchial
10	chr12:123830200-123847600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr12:123830400-123847600	Weak transcription	Aorta	Aorta
12	chr12:123830600-123847600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:123830800-123847200	Weak transcription	Hela-S3	cervix
14	chr12:123830800-123847200	Weak transcription	HSMMtube	muscle
15	chr12:123832400-123848200	Weak transcription	Esophagus	oesophagus
16	chr12:123832800-123847000	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:123832800-123847000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr12:123832800-123847200	Weak transcription	Brain Anterior Caudate	brain
19	chr12:123832800-123847400	Weak transcription	Osteobl	bone
20	chr12:123832800-123847800	Weak transcription	Fetal Kidney	kidney
21	chr12:123833000-123847000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:123833000-123847000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:123833800-123847600	Weak transcription	NH-A	brain
24	chr12:123834000-123847000	Weak transcription	Adipose Nuclei	Adipose
25	chr12:123834200-123847000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr12:123834200-123847400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:123834200-123847400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr12:123834200-123847400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr12:123834600-123847400	Weak transcription	NHEK	skin
30	chr12:123834800-123847000	Weak transcription	Placenta	Placenta
31	chr12:123834800-123847600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:123835000-123847400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:123835000-123847400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:123835000-123847400	Weak transcription	Thymus	Thymus
35	chr12:123835000-123847800	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr12:123835000-123848200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:123835200-123847600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:123835400-123847400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:123835400-123847800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr12:123835400-123847800	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:123836000-123848200	Weak transcription	Gastric	stomach
42	chr12:123837400-123847200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:123837800-123847000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:123838800-123847400	Weak transcription	Colon Smooth Muscle	Colon
45	chr12:123839400-123847000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr12:123839400-123847000	Weak transcription	HepG2	liver
47	chr12:123840600-123847000	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:123840600-123847200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr12:123840800-123847000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr12:123840800-123847200	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links