Variant report

Variant	rs11189328
Chromosome Location	chr10:99448004-99448005
allele	C/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	TCF12	chr10:99445917-99448668	A549	lung:	n/a	n/a
2	TBL1XR1	chr10:99446982-99448314	K562	blood:	n/a	n/a
3	HEY1	chr10:99446631-99448474	HepG2	liver:	n/a	chr10:99447233-99447242
4	ARID3A	chr10:99447765-99448282	HepG2	liver:	n/a	n/a
5	RAD21	chr10:99447990-99448390	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr10:99446514-99448595	Hela-S3	cervix:	n/a	n/a
7	KAP1	chr10:99446150-99448574	HEK293	kidney:	n/a	n/a
8	POLR2A	chr10:99446301-99448203	PBDE	blood:	n/a	n/a
9	SIX5	chr10:99447277-99448777	A549	lung:	n/a	n/a
10	MYC	chr10:99446682-99448481	MCF10A-Er-Src	breast:	n/a	chr10:99447087-99447097 chr10:99447062-99447072 chr10:99447395-99447404 chr10:99447395-99447405
11	SP1	chr10:99446093-99448530	A549	lung:	n/a	chr10:99447161-99447171 chr10:99447276-99447288 chr10:99447276-99447288 chr10:99447080-99447092 chr10:99447161-99447171 chr10:99447068-99447078 chr10:99447080-99447092 chr10:99447278-99447287 chr10:99447087-99447099 chr10:99447179-99447193 chr10:99447081-99447095 chr10:99447068-99447078 chr10:99447081-99447090 chr10:99447082-99447091 chr10:99447277-99447286 chr10:99447089-99447098 chr10:99447081-99447090
12	PRDM1	chr10:99447673-99448434	Hela-S3	cervix:	n/a	n/a
13	FOS	chr10:99447990-99448333	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr10:99447602-99448326	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr10:99446635-99448307	HepG2	liver:	n/a	n/a
16	TBP	chr10:99446791-99448499	Hela-S3	cervix:	n/a	n/a
17	HCFC1	chr10:99445863-99448793	Hela-S3	cervix:	n/a	n/a
18	STAT3	chr10:99447983-99448326	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr10:99446416-99448434	HepG2	liver:	n/a	n/a
20	MYC	chr10:99446552-99448244	K562	blood:	n/a	chr10:99447087-99447097 chr10:99447062-99447072 chr10:99447395-99447404 chr10:99447395-99447405
21	MAFF	chr10:99447929-99448326	HepG2	liver:	n/a	chr10:99448148-99448166
22	TBP	chr10:99446179-99448260	HepG2	liver:	n/a	n/a
23	POLR2A	chr10:99444791-99448454	IMR90	lung:	n/a	n/a
24	E2F4	chr10:99448001-99448279	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr10:99446087-99448503	Hela-S3	cervix:	n/a	chr10:99447087-99447097 chr10:99447062-99447072 chr10:99447395-99447404 chr10:99447395-99447405
26	TAF1	chr10:99447909-99448273	Hela-S3	cervix:	n/a	n/a
27	HEY1	chr10:99447753-99448159	HepG2	liver:	n/a	n/a
28	MAZ	chr10:99447915-99448318	K562	blood:	n/a	n/a
29	RCOR1	chr10:99446088-99448423	Hela-S3	cervix:	n/a	n/a
30	CEBPB	chr10:99447930-99448378	IMR90	lung:	n/a	chr10:99448167-99448178
31	SP1	chr10:99446645-99448594	A549	lung:	n/a	chr10:99447161-99447171 chr10:99447276-99447288 chr10:99447276-99447288 chr10:99447080-99447092 chr10:99447161-99447171 chr10:99447068-99447078 chr10:99447080-99447092 chr10:99447278-99447287 chr10:99447087-99447099 chr10:99447179-99447193 chr10:99447081-99447095 chr10:99447068-99447078 chr10:99447081-99447090 chr10:99447082-99447091 chr10:99447277-99447286 chr10:99447089-99447098 chr10:99447081-99447090
32	RFX5	chr10:99446800-99448492	Hela-S3	cervix:	n/a	n/a
33	SMARCC1	chr10:99446029-99448500	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr10:99447895-99448301	K562	blood:	n/a	n/a
35	POLR2A	chr10:99446418-99448462	HepG2	liver:	n/a	n/a
36	MYC	chr10:99447715-99448326	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr10:99447768-99448401	Hela-S3	cervix:	n/a	chr10:99448359-99448366
38	POLR2A	chr10:99444874-99448472	MCF10A-Er-Src	breast:	n/a	n/a
39	SMC3	chr10:99446077-99448459	Hela-S3	cervix:	n/a	n/a
40	CHD2	chr10:99446656-99448402	Hela-S3	cervix:	n/a	n/a
41	MAZ	chr10:99446015-99448718	IMR90	lung:	n/a	chr10:99446067-99446076 chr10:99447087-99447097 chr10:99447062-99447072 chr10:99447395-99447404 chr10:99447395-99447405
42	MAFK	chr10:99447977-99448335	HepG2	liver:	n/a	chr10:99448149-99448165 chr10:99448153-99448164 chr10:99448154-99448165 chr10:99448154-99448165 chr10:99448152-99448166 chr10:99448149-99448164 chr10:99448153-99448164
43	JUND	chr10:99447835-99448423	Hela-S3	cervix:	n/a	n/a
44	CEBPB	chr10:99446579-99448474	Hela-S3	cervix:	n/a	chr10:99448167-99448178
45	MYC	chr10:99447887-99448186	K562	blood:	n/a	n/a
46	MAX	chr10:99445929-99448401	HCT-116	colon:	n/a	chr10:99446067-99446076 chr10:99447087-99447097 chr10:99447062-99447072 chr10:99447395-99447404 chr10:99447395-99447405
47	CEBPB	chr10:99447892-99448475	A549	lung:	n/a	chr10:99448167-99448178
48	NR3C1	chr10:99447941-99448428	A549	lung:	n/a	n/a
49	HNF4A	chr10:99446469-99448317	HepG2	liver:	n/a	n/a
50	POLR2A	chr10:99447864-99448351	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99447210..99448718-chr10:99495908..99497719,2	K562	blood:
2	chr10:99447448..99448100-chr12:108956001..108956606,2	Hela-S3	cervix:
3	chr10:99447404..99448230-chr17:27467116..27467621,2	Hela-S3	cervix:
4	chr10:99433977..99435889-chr10:99447100..99448771,2	K562	blood:
5	chr10:99446145..99449629-chr10:99495749..99499452,3	K562	blood:
6	chr10:99446266..99448824-chr10:99470047..99473651,4	K562	blood:
7	chr10:99445750..99450066-chr10:99494053..99497713,5	MCF-7	breast:
8	chr10:99444910..99448624-chr10:99472151..99475238,4	K562	blood:
9	chr10:99446264..99449966-chr10:99495266..99498485,3	MCF-7	breast:
10	chr10:99399087..99401527-chr10:99446729..99449313,3	MCF-7	breast:
11	chr10:99442762..99448311-chr10:99470830..99475549,8	MCF-7	breast:
12	chr10:99447297..99448187-chr20:30192642..30193144,2	Hela-S3	cervix:
13	chr10:99443080..99453237-chr10:99471420..99478243,12	MCF-7	breast:

Variant related genes	Relation type
AVPI1	TF binding region
ENSG00000125968	Chromatin interaction
ENSG00000263709	Chromatin interaction
ENSG00000196535	Chromatin interaction
ENSG00000155256	Chromatin interaction
ENSG00000136003	Chromatin interaction
ENSG00000155254	Chromatin interaction
ENSG00000155252	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10882987	1.00[CEU][hapmap]
rs10882990	0.84[CEU][hapmap]
rs11189312	1.00[CEU][hapmap]
rs11189321	1.00[CEU][hapmap]
rs11189331	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12218718	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2065672	1.00[CEU][hapmap]
rs3818780	1.00[CEU][hapmap]
rs7072085	1.00[CEU][hapmap]
rs7896659	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7908082	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7908350	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7922721	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9787703	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer 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 target site	66 gene(s)	inside rSNPs	diseases
2	nsv1045292	chr10:99411153-99450861	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11189328	FRAT2	cis	cerebellum	SCAN
rs11189328	DHDPSL	cis	cerebellum	SCAN
rs11189328	ZFYVE27	cis	cerebellum	SCAN
rs11189328	C10orf62	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99444600-99448200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr10:99444800-99448400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr10:99446800-99448400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr10:99447000-99449400	Weak transcription	Gastric	stomach
5	chr10:99447000-99451200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:99447200-99449400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:99447400-99448200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr10:99447400-99448200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr10:99447400-99448200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr10:99447400-99448200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr10:99447400-99448200	Flanking Active TSS	Liver	Liver
12	chr10:99447400-99448200	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr10:99447400-99448200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr10:99447400-99448200	Flanking Active TSS	Fetal Lung	lung
15	chr10:99447400-99448200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
16	chr10:99447400-99448200	Flanking Active TSS	Stomach Smooth Muscle	stomach
17	chr10:99447400-99448200	Flanking Active TSS	Dnd41	blood
18	chr10:99447400-99448200	Flanking Active TSS	HSMM	muscle
19	chr10:99447400-99448400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
20	chr10:99447400-99448400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
21	chr10:99447400-99448400	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr10:99447400-99448400	Flanking Active TSS	HepG2	liver
23	chr10:99447400-99448400	Flanking Active TSS	K562	blood
24	chr10:99447400-99448600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr10:99447400-99448600	Flanking Active TSS	A549	lung
26	chr10:99447400-99448600	Flanking Active TSS	Hela-S3	cervix
27	chr10:99447400-99448800	Enhancers	Spleen	Spleen
28	chr10:99447600-99448200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:99447600-99448200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:99447600-99448200	Enhancers	Aorta	Aorta
31	chr10:99447600-99448200	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr10:99447600-99448200	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr10:99447600-99448200	Enhancers	Colonic Mucosa	Colon
34	chr10:99447600-99448200	Enhancers	Pancreas	Pancrea
35	chr10:99447600-99448400	Enhancers	Primary hematopoietic stem cells	blood
36	chr10:99447600-99448400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:99447600-99448400	Enhancers	Left Ventricle	heart
38	chr10:99447600-99448400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr10:99447600-99448600	Enhancers	Right Ventricle	heart
40	chr10:99447600-99448800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr10:99447600-99449200	Enhancers	NHEK	skin
42	chr10:99447600-99449400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr10:99447600-99449800	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr10:99447600-99450200	Enhancers	Placenta	Placenta
45	chr10:99447600-99451000	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr10:99447600-99451000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr10:99447600-99451000	Enhancers	HMEC	breast
48	chr10:99447800-99448200	Enhancers	Brain Anterior Caudate	brain
49	chr10:99447800-99448200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
50	chr10:99447800-99448200	Active TSS	Fetal Brain Male	brain

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