Variant report

Variant	rs9836178
Chromosome Location	chr3:52925403-52925404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:52900488..52902600-chr3:52922846..52925520,2	MCF-7	breast:
2	chr3:52925161..52929038-chr3:52929982..52933172,4	MCF-7	breast:
3	chr3:52924236..52926036-chr3:53079854..53081517,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction
ENSG00000248592	Chromatin interaction
ENSG00000213533	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11130332	0.81[EUR][1000 genomes]
rs1134546	0.91[EUR][1000 genomes]
rs11708223	0.80[EUR][1000 genomes]
rs13082061	0.81[EUR][1000 genomes]
rs2336162	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336666	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2581797	0.81[EUR][1000 genomes]
rs2581801	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2581802	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2581805	0.80[EUR][1000 genomes]
rs2581810	0.84[EUR][1000 genomes]
rs2581815	0.81[EUR][1000 genomes]
rs2710342	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2710345	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2878762	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4302374	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4687559	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687560	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445547	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773040	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797399	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7621939	0.80[EUR][1000 genomes]
rs9682464	0.82[AMR][1000 genomes]
rs9831409	0.81[EUR][1000 genomes]
rs9839035	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9844736	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847024	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9876403	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9836178	MUSTN1	cis	Artery Aorta	GTEx
rs9836178	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9836178	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9836178	ITIH4-AS1	cis	lung	GTEx
rs9836178	ITIH4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
2	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:52908400-52930600	Weak transcription	A549	lung
5	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:52910000-52929400	Weak transcription	HMEC	breast
7	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:52910600-52926400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:52913200-52926600	Weak transcription	K562	blood
15	chr3:52916400-52930600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:52916600-52926000	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:52917000-52926000	Weak transcription	Psoas Muscle	Psoas
18	chr3:52918400-52926000	Weak transcription	Small Intestine	intestine
19	chr3:52919200-52930200	Weak transcription	Fetal Kidney	kidney
20	chr3:52919800-52926000	Weak transcription	HSMM	muscle
21	chr3:52920000-52926600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:52920000-52929200	Weak transcription	Dnd41	blood
23	chr3:52920200-52925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:52920200-52929400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:52920200-52929800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:52920400-52925800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:52920400-52925800	Weak transcription	Left Ventricle	heart
28	chr3:52920400-52926600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:52920400-52930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52920400-52930600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52920400-52930600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr3:52921600-52926400	Weak transcription	Spleen	Spleen
33	chr3:52921600-52930600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:52921800-52926400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:52921800-52926400	Weak transcription	Right Atrium	heart
36	chr3:52921800-52926600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:52921800-52927800	Weak transcription	Right Ventricle	heart
38	chr3:52923200-52925600	Strong transcription	Brain Germinal Matrix	brain
39	chr3:52923400-52926400	Weak transcription	Lung	lung
40	chr3:52923400-52927400	Enhancers	Fetal Lung	lung
41	chr3:52923800-52928800	Enhancers	Brain Cingulate Gyrus	brain
42	chr3:52924000-52925600	Enhancers	Brain Angular Gyrus	brain
43	chr3:52924000-52927200	Enhancers	Pancreas	Pancrea
44	chr3:52924000-52929400	Enhancers	Brain Hippocampus Middle	brain
45	chr3:52924000-52930000	Enhancers	Brain Substantia Nigra	brain
46	chr3:52924200-52926600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:52924200-52926600	Enhancers	Liver	Liver
48	chr3:52924200-52927200	Enhancers	Gastric	stomach
49	chr3:52924200-52930200	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr3:52924400-52926000	Enhancers	NHDF-Ad	bronchial

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