Variant report

Variant	rs3814316
Chromosome Location	chr1:155149718-155149719
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	CTCF	chr1:155149660-155149810	GM12869	blood:	n/a	n/a
2	RAD21	chr1:155148311-155149729	SK-N-SH	brain:	n/a	chr1:155148747-155148761 chr1:155149265-155149277 chr1:155149302-155149314 chr1:155149261-155149270 chr1:155149260-155149279
3	SMC3	chr1:155148721-155150293	SK-N-SH	brain:	n/a	chr1:155149947-155149957 chr1:155149261-155149275 chr1:155149265-155149275 chr1:155149259-155149273 chr1:155149261-155149269
4	HDAC2	chr1:155149601-155150149	MCF-7	breast:	n/a	n/a
5	FOXA1	chr1:155149683-155149987	T-47D	breast:	n/a	n/a
6	CTCF	chr1:155149097-155149723	K562	blood:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
7	ELF1	chr1:155149062-155150568	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:155148339-155149824	HCT-116	colon:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
9	EP300	chr1:155149637-155150114	T-47D	breast:	n/a	chr1:155149944-155149960
10	MAX	chr1:155148372-155150327	MCF-7	breast:	n/a	chr1:155150204-155150213 chr1:155150227-155150236
11	NR2F2	chr1:155149174-155150157	MCF-7	breast:	n/a	n/a
12	MYC	chr1:155149717-155149972	MCF-7	breast:	n/a	n/a
13	ESR1	chr1:155149665-155150073	T-47D	breast:	n/a	n/a
14	NR2F2	chr1:155149019-155150289	MCF-7	breast:	n/a	n/a
15	EP300	chr1:155149558-155150170	T-47D	breast:	n/a	chr1:155149944-155149960
16	HDAC2	chr1:155149578-155150244	MCF-7	breast:	n/a	n/a
17	CTCF	chr1:155149600-155149750	Caco-2	colon:	n/a	n/a
18	GATA3	chr1:155149577-155150062	T-47D	breast:	n/a	chr1:155149815-155149825
19	MAX	chr1:155149467-155150165	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:155148890-155150419	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:155147446-155152948	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr1:155149613-155150073	T-47D	breast:	n/a	chr1:155149815-155149825
23	CTCF	chr1:155148182-155149735	A549	lung:	n/a	chr1:155149262-155149271 chr1:155149261-155149282 chr1:155149264-155149274 chr1:155149285-155149294 chr1:155149260-155149276 chr1:155149259-155149277 chr1:155149262-155149275
24	GATA3	chr1:155149632-155149950	MCF-7	breast:	n/a	chr1:155149815-155149825
25	STAT3	chr1:155149717-155149725	GM12878	blood:	n/a	n/a
26	EBF1	chr1:155149140-155149739	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155149130..155149875-chr1:155176389..155177179,2	MCF-7	breast:
2	chr1:155143901..155153030-chr1:155191166..155199183,23	MCF-7	breast:
3	chr1:155059639..155063596-chr1:155149285..155151101,3	MCF-7	breast:
4	chr1:155149084..155150074-chr1:155196318..155196838,2	MCF-7	breast:
5	chr1:155148823..155149771-chr1:155196116..155196635,2	K562	blood:
6	chr1:155148758..155149726-chr1:155162834..155163883,7	K562	blood:
7	chr1:155149492..155150014-chr1:155161259..155161836,2	MCF-7	breast:
8	chr1:155064648..155066932-chr1:155147928..155150182,2	K562	blood:
9	chr1:155148380..155150190-chr1:155292147..155294545,2	MCF-7	breast:
10	chr1:155095314..155110392-chr1:155134312..155151496,72	MCF-7	breast:
11	chr1:155148507..155150033-chr1:155162898..155164095,27	MCF-7	breast:
12	chr1:155066706..155067679-chr1:155149226..155149765,2	MCF-7	breast:
13	chr1:155148301..155150189-chr1:155162933..155164249,12	MCF-7	breast:
14	chr1:155148862..155150825-chr1:155499842..155501461,2	MCF-7	breast:
15	chr1:155111752..155114583-chr1:155147267..155150123,4	MCF-7	breast:
16	chr1:155140056..155140720-chr1:155149675..155150429,2	K562	blood:
17	chr1:155140499..155142005-chr1:155147734..155150654,2	K562	blood:
18	chr1:155148495..155149762-chr1:155196236..155196972,5	MCF-7	breast:
19	chr1:155105664..155110180-chr1:155143584..155151850,15	MCF-7	breast:
20	chr1:155148304..155150985-chr1:155195622..155198249,4	K562	blood:
21	chr1:155149535..155150526-chr1:155162691..155163480,2	MCF-7	breast:
22	chr1:155062424..155064059-chr1:155147918..155149990,2	K562	blood:
23	chr1:155035026..155037423-chr1:155149492..155151258,2	MCF-7	breast:
24	chr1:155149010..155149798-chr1:155292525..155293331,4	K562	blood:
25	chr1:155148972..155149720-chr1:155171461..155172174,2	MCF-7	breast:
26	chr1:155094769..155105017-chr1:155135344..155151845,46	MCF-7	breast:
27	chr1:155149477..155151291-chr1:155230798..155233673,2	MCF-7	breast:
28	chr1:155110723..155114225-chr1:155147854..155154401,7	K562	blood:
29	chr1:155149492..155150044-chr1:155161179..155161836,3	MCF-7	breast:
30	chr1:155146416..155150261-chr1:155194777..155198198,7	MCF-7	breast:
31	chr1:155053097..155054666-chr1:155148381..155150762,2	MCF-7	breast:

Variant related genes	Relation type
KRTCAP2	TF binding region
ENSG00000160766	Chromatin interaction
ENSG00000243364	Chromatin interaction
ENSG00000169231	Chromatin interaction
ENSG00000116521	Chromatin interaction
ENSG00000169241	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000160753	Chromatin interaction
ENSG00000225855	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000185499	Chromatin interaction
ENSG00000179085	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10157801	0.86[CHB][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs1057941	0.87[ASN][1000 genomes]
rs10908458	0.86[CHB][hapmap]
rs11264337	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs11264338	0.86[CHB][hapmap];0.84[CHD][hapmap];0.82[JPT][hapmap]
rs11264339	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs11264341	0.87[ASW][hapmap];0.83[CHD][hapmap];0.88[LWK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]
rs11799962	0.85[AMR][1000 genomes]
rs12025371	0.86[CHB][hapmap]
rs12028043	0.86[CHB][hapmap];0.82[CHD][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes]
rs12127609	0.84[AMR][1000 genomes]
rs12904	0.85[CHB][hapmap]
rs2066981	0.81[JPT][hapmap]
rs2070803	0.93[ASN][1000 genomes]
rs2075571	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs34257409	0.85[AMR][1000 genomes]
rs4072037	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs423144	0.86[ASN][1000 genomes]
rs4246529	0.86[CHB][hapmap];0.84[MEX][hapmap]
rs4276913	0.86[CHB][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs4276914	0.81[ASN][1000 genomes]
rs4421576	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4460629	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs4745	0.86[CHB][hapmap]
rs4971059	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971066	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs4971073	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap]
rs4971076	0.85[AMR][1000 genomes]
rs4971079	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs4971085	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4971088	0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs4971089	0.81[ASN][1000 genomes]
rs4971091	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4971093	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971099	0.84[ASN][1000 genomes]
rs4971100	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4971101	0.93[ASN][1000 genomes]
rs7364524	0.85[AMR][1000 genomes]
rs7366775	0.85[ASN][1000 genomes]
rs7556304	0.86[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs914615	0.91[JPT][hapmap]
rs9297	0.86[CHB][hapmap];0.84[MEX][hapmap]
rs9426886	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	esv1823746	chr1:154965207-155231904	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
3	nsv464084	chr1:155082298-155194980	Weak transcription Bivalent Enhancer Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
4	nsv547961	chr1:155082298-155194980	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	366 gene(s)	inside rSNPs	diseases
5	nsv831614	chr1:155094978-155275031	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	434 gene(s)	inside rSNPs	diseases
6	esv2757756	chr1:155094978-155314807	Bivalent Enhancer Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
7	esv2758971	chr1:155094978-155314807	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	452 gene(s)	inside rSNPs	diseases
8	nsv470741	chr1:155115260-155230131	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	381 gene(s)	inside rSNPs	diseases
9	nsv1010146	chr1:155119096-155201064	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
10	nsv872457	chr1:155135335-155310443	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	407 gene(s)	inside rSNPs	diseases
11	nsv8447	chr1:155144629-155156937	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
12	nsv831625	chr1:155145634-155313409	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	407 gene(s)	inside rSNPs	diseases
13	nsv872458	chr1:155146102-155180466	Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	316 gene(s)	inside rSNPs	diseases
14	nsv872459	chr1:155149718-155169633	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	308 gene(s)	inside rSNPs	diseases
15	nsv527682	chr1:155149718-155197462	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	361 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3814316	MUC1	cis	lymphoblastoid	seeQTL
rs3814316	MEIS2	trans	lymphoblastoid	seeQTL
rs3814316	C1orf56	cis	parietal	SCAN
rs3814316	MUC1	cis	Esophagus Mucosa	GTEx
rs3814316	UBE2Q1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155146400-155157600	Weak transcription	Right Atrium	heart
2	chr1:155146600-155163000	Weak transcription	Aorta	Aorta
3	chr1:155146800-155150400	Enhancers	GM12878-XiMat	blood
4	chr1:155146800-155150800	Enhancers	Gastric	stomach
5	chr1:155147200-155149800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr1:155147600-155149800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:155147600-155149800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:155147600-155151600	Weak transcription	Osteobl	bone
9	chr1:155147600-155157200	Weak transcription	Right Ventricle	heart
10	chr1:155147800-155149800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:155147800-155149800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:155148000-155150000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:155148000-155150400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr1:155148000-155150600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:155148000-155150800	Weak transcription	NH-A	brain
16	chr1:155148200-155149800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:155148400-155149800	Enhancers	Duodenum Mucosa	Duodenum
18	chr1:155148400-155149800	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:155148400-155150000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:155148400-155157800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:155148600-155149800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:155148600-155150000	Enhancers	HepG2	liver
23	chr1:155148800-155150000	Enhancers	Hela-S3	cervix
24	chr1:155148800-155150200	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:155148800-155154800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:155148800-155155200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr1:155149000-155149800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:155149000-155149800	Enhancers	Colon Smooth Muscle	Colon
29	chr1:155149000-155150400	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr1:155149000-155152600	Enhancers	Stomach Mucosa	stomach
31	chr1:155149000-155155400	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:155149200-155149800	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr1:155149200-155149800	Enhancers	Primary B cells from peripheral blood	blood
34	chr1:155149200-155149800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr1:155149200-155149800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:155149200-155149800	Enhancers	Fetal Intestine Small	intestine
37	chr1:155149200-155149800	Enhancers	Fetal Lung	lung
38	chr1:155149200-155149800	Enhancers	Fetal Muscle Trunk	muscle
39	chr1:155149200-155149800	Enhancers	Lung	lung
40	chr1:155149200-155149800	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr1:155149200-155149800	Genic enhancers	Thymus	Thymus
42	chr1:155149200-155149800	Flanking Active TSS	Dnd41	blood
43	chr1:155149200-155150000	Enhancers	NHEK	skin
44	chr1:155149200-155150200	Enhancers	Pancreas	Pancrea
45	chr1:155149200-155150400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:155149200-155152200	Enhancers	Placenta	Placenta
47	chr1:155149200-155152800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr1:155149400-155149800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr1:155149400-155149800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr1:155149400-155149800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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