Variant report

Variant	rs10746973
Chromosome Location	chr9:71555492-71555493
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	POLR2A	chr9:71555427-71555943	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr9:71555439-71556061	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
RNU6-820P	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10114872	0.86[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs10115608	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10117043	0.91[GIH][hapmap]
rs10117188	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10117198	0.86[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10119540	0.86[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056265	0.96[ASN][1000 genomes]
rs10746974	0.81[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10746979	0.85[GIH][hapmap]
rs10781276	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10869578	0.81[EUR][1000 genomes]
rs10869599	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10869623	0.93[CEU][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11144468	0.86[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11144471	0.90[EUR][1000 genomes]
rs11144474	0.92[CEU][hapmap];0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11144476	0.86[GIH][hapmap]
rs11144496	0.93[CEU][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11144510	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs12349586	0.81[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12378665	0.86[MEX][hapmap]
rs12684346	0.88[CHD][hapmap];0.86[MEX][hapmap]
rs12686693	0.90[CHD][hapmap];1.00[MEX][hapmap]
rs17058884	0.90[CHD][hapmap];0.86[MEX][hapmap]
rs57919809	0.86[EUR][1000 genomes]
rs62569165	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62569167	0.84[EUR][1000 genomes]
rs7018692	0.88[GIH][hapmap]
rs7022925	0.91[ASN][1000 genomes]
rs7040120	0.83[GIH][hapmap]
rs7041792	0.86[CEU][hapmap]
rs7852633	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs7859638	0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422258	chr9:71234845-71663340	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1017903	chr9:71276951-71690579	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1051723	chr9:71398713-71971285	Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1053402	chr9:71399722-71819949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv540146	chr9:71399722-71819949	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1043689	chr9:71399922-71800338	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv540147	chr9:71399922-71800338	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv1047540	chr9:71401918-71803639	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv931684	chr9:71417110-71957723	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv1049175	chr9:71418242-71986910	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv466393	chr9:71453443-71704827	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv614547	chr9:71453443-71704827	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv1035823	chr9:71465139-71901672	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
14	nsv466396	chr9:71471912-71935577	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv614548	chr9:71471912-71935577	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv614549	chr9:71506459-71659280	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv1051798	chr9:71511805-71792032	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv1035477	chr9:71511927-71959487	Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
19	esv1833433	chr9:71544920-71598165	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	esv2761530	chr9:71548497-71559537	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10746973	FAM108B1	cis	cerebellum	SCAN
rs10746973	KLF9	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:71510400-71576200	Weak transcription	Stomach Mucosa	stomach
2	chr9:71514200-71557800	Weak transcription	Lung	lung
3	chr9:71519400-71573000	Weak transcription	Gastric	stomach
4	chr9:71532800-71556800	Weak transcription	Right Ventricle	heart
5	chr9:71535000-71569600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:71536600-71557400	Weak transcription	Colonic Mucosa	Colon
7	chr9:71542200-71564400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:71545000-71561600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:71545400-71562400	Weak transcription	K562	blood
10	chr9:71546800-71561000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:71547200-71557400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr9:71548800-71555600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr9:71548800-71564200	Weak transcription	Placenta	Placenta
14	chr9:71549200-71557200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:71549200-71562000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:71549200-71566200	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr9:71549200-71570000	Weak transcription	Fetal Stomach	stomach
18	chr9:71549600-71569600	Weak transcription	Fetal Kidney	kidney
19	chr9:71550600-71556600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:71550800-71555600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr9:71551000-71556000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:71553400-71558600	Strong transcription	Fetal Intestine Large	intestine
23	chr9:71553400-71567200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:71553600-71556200	Strong transcription	Primary B cells from peripheral blood	blood
25	chr9:71553600-71557600	Strong transcription	Duodenum Mucosa	Duodenum
26	chr9:71553600-71557600	Strong transcription	HepG2	liver
27	chr9:71553600-71558000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr9:71553800-71558400	Strong transcription	Primary B cells from cord blood	blood
29	chr9:71553800-71565000	Weak transcription	Pancreas	Pancrea
30	chr9:71554400-71565200	Weak transcription	Small Intestine	intestine
31	chr9:71554400-71569600	Weak transcription	Aorta	Aorta
32	chr9:71554800-71555600	Weak transcription	Primary hematopoietic stem cells	blood
33	chr9:71554800-71558000	Enhancers	Fetal Heart	heart
34	chr9:71555400-71555600	Enhancers	Left Ventricle	heart
35	chr9:71555400-71555800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr9:71555400-71555800	Strong transcription	Fetal Intestine Small	intestine
37	chr9:71555400-71556600	Strong transcription	GM12878-XiMat	blood
38	chr9:71555400-71560800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links