Variant report

Variant	rs935075
Chromosome Location	chr1:9942118-9942119
allele	A/G
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	SIN3AK20	chr1:9941872-9942183	SK-N-SH	brain:	n/a	n/a
2	RUNX3	chr1:9941854-9942142	GM12878	blood:	n/a	chr1:9941969-9941984
3	NFIC	chr1:9941672-9942374	SK-N-SH	brain:	n/a	chr1:9942188-9942205
4	RXRA	chr1:9941708-9942252	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr1:9942020-9942170	AG04450	lung:	n/a	n/a
6	FOS	chr1:9941795-9942189	MCF10A-Er-Src	breast:	n/a	n/a
7	SPI1	chr1:9941951-9942499	HL-60	blood:	n/a	chr1:9942138-9942151
8	NFIC	chr1:9941742-9942488	SK-N-SH	brain:	n/a	chr1:9942188-9942205
9	PBX3	chr1:9941793-9942339	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr1:9941747-9942225	U87	brain:	n/a	n/a
11	MYC	chr1:9941830-9942290	MCF10A-Er-Src	breast:	n/a	n/a
12	TEAD4	chr1:9941834-9942387	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr1:9942045-9942245	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr1:9941804-9942262	MCF10A-Er-Src	breast:	n/a	n/a
15	FOS	chr1:9941805-9942202	MCF10A-Er-Src	breast:	n/a	n/a
16	CTCF	chr1:9942080-9942230	HCPEpiC	choroid plexus:	n/a	n/a
17	FOSL2	chr1:9941724-9942322	SK-N-SH	brain:	n/a	n/a
18	CTCF	chr1:9942080-9942230	HMF	breast:	n/a	n/a
19	GATA3	chr1:9941707-9942435	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr1:9942060-9942210	HPAF	blood vessel:	n/a	n/a
21	POLR2A	chr1:9941811-9942237	U87	brain:	n/a	n/a
22	MYC	chr1:9941832-9942269	MCF10A-Er-Src	breast:	n/a	n/a
23	GATA3	chr1:9941654-9942408	SK-N-SH	brain:	n/a	n/a
24	STAT3	chr1:9941874-9942244	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:9941978..9943694-chr1:9945295..9946902,2	K562	blood:
2	chr1:9940644..9943177-chr1:9967907..9970877,2	K562	blood:
3	chr1:9941062..9943357-chr1:9968591..9972232,3	K562	blood:
4	chr1:9937046..9938732-chr1:9940830..9942579,2	K562	blood:

Variant related genes	Relation type
CTNNBIP1	TF binding region
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1220381	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220382	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1220383	0.80[CEU][hapmap]
rs1220384	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220393	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220394	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs1220395	1.00[CEU][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs1220396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1220404	1.00[MEX][hapmap];0.83[TSI][hapmap];0.90[AMR][1000 genomes]
rs1220405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1220406	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1220411	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1220412	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1220413	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1220418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372106	1.00[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1470160	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs15177	0.84[CHB][hapmap]
rs1660735	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034420	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2083577	0.88[EUR][1000 genomes]
rs2278611	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs2379108	0.90[EUR][1000 genomes]
rs2486084	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2582980	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2582981	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3120822	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3860318	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs3888014	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs6695334	0.84[CHB][hapmap];0.81[CHD][hapmap]
rs7225	0.95[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs935073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935074	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs946275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh 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	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs935075	LOC440563	cis	parietal	SCAN
rs935075	NPPB	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
2	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
3	chr1:9930800-9942200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:9930800-9949600	Weak transcription	Fetal Lung	lung
5	chr1:9932000-9942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:9932200-9942200	Weak transcription	Thymus	Thymus
7	chr1:9932200-9942800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:9932600-9942600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:9932600-9960200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:9932800-9942200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:9933000-9946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:9935400-9942600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:9935400-9942800	Weak transcription	Colonic Mucosa	Colon
14	chr1:9935400-9944200	Weak transcription	Ovary	ovary
15	chr1:9935400-9948800	Weak transcription	Primary B cells from cord blood	blood
16	chr1:9935600-9942200	Weak transcription	Lung	lung
17	chr1:9935600-9943400	Weak transcription	Pancreas	Pancrea
18	chr1:9935600-9948600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:9935600-9949200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:9935600-9949400	Weak transcription	HUVEC	blood vessel
21	chr1:9935600-9950200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:9935600-9960800	Weak transcription	Fetal Intestine Large	intestine
23	chr1:9935800-9944200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:9935800-9946200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:9935800-9946600	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:9935800-9950800	Weak transcription	Aorta	Aorta
27	chr1:9936000-9943000	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:9936000-9946200	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:9936000-9948800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr1:9936000-9950000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:9936000-9950000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:9936200-9949800	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:9936400-9960200	Weak transcription	Liver	Liver
34	chr1:9937200-9950000	Weak transcription	Fetal Brain Male	brain
35	chr1:9937400-9943800	Weak transcription	Brain Anterior Caudate	brain
36	chr1:9937400-9944800	Weak transcription	Right Atrium	heart
37	chr1:9937600-9942400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:9937600-9943600	Weak transcription	Brain Angular Gyrus	brain
39	chr1:9937600-9943600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:9937800-9943600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:9938000-9943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:9938200-9942200	Weak transcription	Brain Germinal Matrix	brain
43	chr1:9938200-9942400	Weak transcription	Spleen	Spleen
44	chr1:9938200-9942600	Weak transcription	Fetal Heart	heart
45	chr1:9938400-9950000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:9938600-9942200	Weak transcription	Placenta	Placenta
47	chr1:9938600-9942600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:9938600-9942800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr1:9938600-9943200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:9938600-9948800	Weak transcription	Placenta Amnion	Placenta Amnion

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