Variant report

Variant	rs1611131
Chromosome Location	chr9:136522187-136522188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SARDH-1	chr9:136519708-136522571	NONHSAT135334

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10993952	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10993953	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10993956	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs129888	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs129915	0.84[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs129927	0.82[EUR][1000 genomes]
rs129928	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2073835	0.89[CEU][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs2073836	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs2073837	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs2519127	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs732833	0.80[MEX][hapmap]
rs7851898	0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv894094	chr9:136311679-136528721	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv530972	chr9:136324358-136643044	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv894100	chr9:136371224-136547602	Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv894106	chr9:136489539-136566959	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv894107	chr9:136494566-136579589	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv894108	chr9:136507473-136617292	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv894109	chr9:136512515-136522985	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv894110	chr9:136512515-136542868	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv466619	chr9:136515297-136528721	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv615640	chr9:136515297-136528721	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1611131	GFI1B	cis	cerebellum	SCAN
rs1611131	BAT2L1	cis	cerebellum	SCAN
rs1611131	CEL	cis	cerebellum	SCAN
rs1611131	ZER1	cis	cerebellum	SCAN
rs1611131	CAMSAP1	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136515000-136523400	Weak transcription	Spleen	Spleen
2	chr9:136520200-136522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr9:136520200-136522800	Enhancers	Brain Germinal Matrix	brain
4	chr9:136520200-136524200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr9:136520400-136523600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:136520400-136525800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr9:136520600-136523000	Weak transcription	Right Atrium	heart
8	chr9:136520800-136523400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr9:136521000-136526600	Enhancers	Liver	Liver
10	chr9:136521200-136522200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr9:136521200-136523000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr9:136521200-136523400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr9:136521200-136523800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr9:136521400-136522200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
15	chr9:136521400-136523000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr9:136521400-136523000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr9:136521400-136525200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr9:136521600-136522200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
19	chr9:136521600-136522200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:136521600-136522400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:136521600-136522400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
22	chr9:136521800-136522200	Bivalent Enhancer	HepG2	liver
23	chr9:136521800-136522400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
24	chr9:136521800-136522400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr9:136521800-136522600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
26	chr9:136521800-136525200	Bivalent Enhancer	Fetal Brain Male	brain
27	chr9:136522000-136522200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr9:136522000-136522200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
29	chr9:136522000-136522200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
30	chr9:136522000-136522400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
31	chr9:136522000-136523600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
32	chr9:136522000-136525200	Bivalent Enhancer	Fetal Muscle Leg	muscle

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