Variant report

Variant	rs11777942
Chromosome Location	chr8:103249111-103249112
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	CHD1	chr8:103248792-103252333	IMR90	lung:	n/a	chr8:103251203-103251213
2	STAT3	chr8:103248816-103249901	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
3	STAT3	chr8:103248790-103249907	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
4	BATF	chr8:103248916-103249176	GM12878	blood:	n/a	chr8:103249039-103249050
5	FOS	chr8:103248863-103249381	MCF10A-Er-Src	breast:	n/a	chr8:103249308-103249317 chr8:103249032-103249044
6	POLR2A	chr8:103248946-103249233	GM12891	blood:	n/a	n/a
7	MYC	chr8:103248904-103249311	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr8:103248892-103249455	MCF10A-Er-Src	breast:	n/a	chr8:103249308-103249317 chr8:103249032-103249044
9	EP300	chr8:103249044-103249192	GM12878	blood:	n/a	n/a
10	EP300	chr8:103248999-103249216	GM12878	blood:	n/a	n/a
11	POLR2A	chr8:103248925-103249285	GM12891	blood:	n/a	n/a
12	STAT1	chr8:103248979-103249174	GM12878	blood:	n/a	n/a
13	POLR2A	chr8:103248763-103252162	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr8:103248931-103249232	SK-N-SH	brain:	n/a	n/a
15	RUNX3	chr8:103248820-103249267	GM12878	blood:	n/a	n/a
16	POLR2A	chr8:103248961-103249222	H1-hESC	embryonic stem cell:	n/a	n/a
17	TBP	chr8:103248891-103249239	GM12878	blood:	n/a	n/a
18	POLR2A	chr8:103248635-103249587	GM12878	blood:	n/a	n/a
19	POLR2A	chr8:103248979-103252107	IMR90	lung:	n/a	n/a
20	POLR2A	chr8:103248965-103249607	GM12891	blood:	n/a	n/a
21	POLR2A	chr8:103248872-103249420	GM12891	blood:	n/a	n/a
22	EBF1	chr8:103248927-103249299	GM12878	blood:	n/a	n/a
23	SPI1	chr8:103248995-103249340	GM12878	blood:	n/a	n/a
24	POLR2A	chr8:103248497-103249913	GM12878	blood:	n/a	n/a
25	STAT3	chr8:103248842-103249488	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
26	CHD1	chr8:103248610-103251204	GM12878	blood:	n/a	n/a
27	POLR2A	chr8:103248725-103251275	GM12891	blood:	n/a	n/a
28	POLR2A	chr8:103248842-103251256	GM12878	blood:	n/a	n/a
29	EBF1	chr8:103248910-103249310	GM12878	blood:	n/a	n/a
30	ZNF143	chr8:103248974-103249264	GM12878	blood:	n/a	n/a
31	WRNIP1	chr8:103249017-103249367	GM12878	blood:	n/a	n/a
32	BATF	chr8:103248881-103249202	GM12878	blood:	n/a	chr8:103249039-103249050
33	STAT3	chr8:103248875-103250310	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
34	MXI1	chr8:103248954-103249451	GM12878	blood:	n/a	n/a
35	CHD2	chr8:103249016-103249206	GM12878	blood:	n/a	n/a
36	EBF1	chr8:103248909-103249328	GM12878	blood:	n/a	n/a
37	POLR2A	chr8:103248887-103252665	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr8:103248883-103249255	GM12892	blood:	n/a	n/a
39	FOS	chr8:103248824-103249384	MCF10A-Er-Src	breast:	n/a	chr8:103249308-103249317 chr8:103249032-103249044
40	MYC	chr8:103248895-103249297	MCF10A-Er-Src	breast:	n/a	n/a
41	SPI1	chr8:103248968-103249389	HL-60	blood:	n/a	n/a
42	FOS	chr8:103248890-103249246	MCF10A-Er-Src	breast:	n/a	chr8:103249032-103249044
43	SPI1	chr8:103248856-103249488	HL-60	blood:	n/a	n/a
44	IKZF1	chr8:103248931-103249330	GM12878	blood:	n/a	n/a
45	STAT3	chr8:103248643-103249469	MCF10A-Er-Src	breast:	n/a	chr8:103249108-103249119
46	POLR2A	chr8:103248985-103249226	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:102505170..102507558-chr8:103249030..103250734,2	MCF-7	breast:
2	chr8:103248705..103250283-chr8:103601762..103604480,2	K562	blood:
3	chr8:103248364..103250740-chr8:103821721..103824052,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000246263	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1037699	0.82[EUR][1000 genomes]
rs1037700	0.84[EUR][1000 genomes]
rs10505019	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1052069	1.00[ASW][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1052071	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11774420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774772	1.00[GIH][hapmap]
rs11776865	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11778107	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11783467	0.93[ASN][1000 genomes]
rs11784180	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11784534	0.81[ASN][1000 genomes]
rs11785514	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11786397	0.81[ASN][1000 genomes]
rs13261195	1.00[GIH][hapmap]
rs16869269	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs16869276	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16869282	1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs16869295	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16918482	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2305832	1.00[GIH][hapmap]
rs2387995	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928571	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28928592	0.93[ASN][1000 genomes]
rs28928597	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28999671	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28999676	0.93[ASN][1000 genomes]
rs28999706	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29000274	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29000286	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs29000294	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35693157	0.88[EUR][1000 genomes]
rs3735720	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735721	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3735722	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907099	0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4329248	0.81[ASN][1000 genomes]
rs5005121	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57901015	0.81[ASN][1000 genomes]
rs60604862	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs718165	1.00[GIH][hapmap]
rs7836046	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7841131	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020359	chr8:103109921-103318415	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033829	chr8:103110057-103525696	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1021459	chr8:103163436-103401754	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv539701	chr8:103163436-103401754	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1025935	chr8:103199207-103468322	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1018990	chr8:103207922-103357742	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv539702	chr8:103207922-103357742	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1028890	chr8:103207922-103401754	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv891242	chr8:103210971-103282418	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
10	nsv891243	chr8:103219629-103292724	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11777942	NCALD	cis	lymphoblastoid	seeQTL
rs11777942	RRM2B	cis	multi-tissue	Pritchard
rs11777942	RRM2B	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:103231600-103249800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:103234600-103250000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr8:103241000-103249200	Weak transcription	Colonic Mucosa	Colon
4	chr8:103241000-103250400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr8:103241000-103250400	Weak transcription	Esophagus	oesophagus
6	chr8:103241400-103249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr8:103241400-103250600	Weak transcription	Spleen	Spleen
8	chr8:103242000-103249400	Weak transcription	Fetal Stomach	stomach
9	chr8:103242600-103249200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr8:103243400-103249800	Weak transcription	Fetal Kidney	kidney
11	chr8:103243600-103249200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr8:103243600-103250200	Weak transcription	Placenta	Placenta
13	chr8:103243800-103249200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr8:103243800-103249800	Weak transcription	Brain Germinal Matrix	brain
15	chr8:103244000-103249800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr8:103244400-103250400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr8:103246800-103249200	Weak transcription	Fetal Intestine Small	intestine
18	chr8:103247600-103249200	Enhancers	Fetal Brain Male	brain
19	chr8:103248000-103249200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr8:103248000-103249200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr8:103248000-103249200	Enhancers	Left Ventricle	heart
22	chr8:103248000-103249400	Enhancers	Colon Smooth Muscle	Colon
23	chr8:103248000-103249600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr8:103248000-103250000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr8:103248000-103250200	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr8:103248000-103250800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr8:103248200-103249200	Enhancers	Brain Anterior Caudate	brain
28	chr8:103248200-103249400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr8:103248200-103249400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr8:103248200-103249400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr8:103248200-103249600	Enhancers	HepG2	liver
32	chr8:103248200-103250000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr8:103248200-103250000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr8:103248200-103250000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr8:103248200-103250000	Enhancers	Adipose Nuclei	Adipose
36	chr8:103248200-103250000	Enhancers	Brain Angular Gyrus	brain
37	chr8:103248400-103249200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr8:103248400-103249200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr8:103248400-103249200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr8:103248400-103249400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr8:103248400-103249400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr8:103248400-103249400	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr8:103248400-103249600	Enhancers	Primary T cells from cord blood	blood
44	chr8:103248400-103249600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr8:103248400-103249600	Weak transcription	Stomach Mucosa	stomach
46	chr8:103248400-103249600	Enhancers	K562	blood
47	chr8:103248400-103249800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr8:103248400-103249800	Enhancers	Small Intestine	intestine
49	chr8:103248400-103250000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr8:103248400-103250200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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