Variant report

Variant	rs9683109
Chromosome Location	chr3:150863781-150863782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150803713..150804925-chr3:150863548..150864359,3	MCF-7	breast:
2	chr3:150480168..150482744-chr3:150863449..150865397,2	MCF-7	breast:
3	chr3:150784764..150785338-chr3:150863570..150864390,2	MCF-7	breast:
4	chr3:150834592..150835523-chr3:150863486..150864448,3	MCF-7	breast:
5	chr3:150784535..150785084-chr3:150863565..150864073,3	K562	blood:
6	chr3:150439130..150439717-chr3:150863762..150864408,2	K562	blood:
7	chr3:150726245..150727142-chr3:150863441..150864471,12	MCF-7	breast:
8	chr3:150803865..150806747-chr3:150863214..150865555,2	MCF-7	breast:
9	chr3:150802905..150803783-chr3:150863612..150864716,6	MCF-7	breast:
10	chr3:150726303..150727160-chr3:150863474..150864399,6	MCF-7	breast:
11	chr3:150726263..150727081-chr3:150863546..150864127,2	K562	blood:
12	chr3:150643163..150644188-chr3:150863256..150864452,7	MCF-7	breast:
13	chr3:150859764..150861987-chr3:150862160..150864120,2	MCF-7	breast:
14	chr3:150784607..150785620-chr3:150863485..150864424,9	MCF-7	breast:
15	chr3:150643602..150644107-chr3:150863509..150864363,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000144893	Chromatin interaction
ENSG00000181788	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1003246	0.87[EUR][1000 genomes]
rs1005726	0.94[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs10755104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10935825	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10935827	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935828	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11914598	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11919212	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12489984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13434276	0.88[ASN][1000 genomes]
rs1346943	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1431492	0.86[EUR][1000 genomes]
rs1431493	0.87[EUR][1000 genomes]
rs16863172	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1835668	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1897296	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1920392	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2014240	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2060081	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs28594277	0.81[EUR][1000 genomes]
rs28690162	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3773615	0.94[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3915228	1.00[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs61184267	0.87[EUR][1000 genomes]
rs6414377	0.88[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440721	0.85[EUR][1000 genomes]
rs6765294	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs6765711	0.82[JPT][hapmap]
rs6767918	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6772640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6780053	0.80[MEX][hapmap]
rs6780120	0.87[EUR][1000 genomes]
rs6787683	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6790661	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6800064	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6801591	0.87[EUR][1000 genomes]
rs6809388	0.89[CEU][hapmap]
rs6809705	0.89[CEU][hapmap];0.84[TSI][hapmap]
rs7427471	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs747205	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633492	0.85[EUR][1000 genomes]
rs7645665	1.00[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs9289832	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs965843	0.86[ASN][1000 genomes]
rs970235	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9813224	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822304	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9823077	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs9829728	1.00[CEU][hapmap]
rs9848163	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9850016	0.90[ASN][1000 genomes]
rs9876500	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9883677	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829756	chr3:150692636-150889738	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9683109	CLRN1	cis	parietal	SCAN
rs9683109	DHX36	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150827400-150873000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:150861200-150865000	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr3:150861400-150872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150861800-150864000	Weak transcription	Fetal Kidney	kidney
5	chr3:150861800-150872600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:150862000-150872200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:150862200-150864000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr3:150862400-150864200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:150862600-150864200	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:150862600-150864200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:150862600-150864400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:150862600-150864400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:150862600-150864400	Enhancers	Primary B cells from peripheral blood	blood
14	chr3:150862800-150865000	Enhancers	Fetal Intestine Small	intestine
15	chr3:150862800-150873000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:150862800-150873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:150863000-150863800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:150863000-150864200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:150863000-150864400	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr3:150863000-150864800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:150863200-150864200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:150863200-150889000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:150863400-150863800	Bivalent Enhancer	HUVEC	blood vessel
24	chr3:150863400-150864200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr3:150863400-150864800	Enhancers	Fetal Intestine Large	intestine
26	chr3:150863600-150863800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:150863600-150863800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr3:150863600-150863800	Bivalent Enhancer	Colonic Mucosa	Colon
29	chr3:150863600-150863800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
30	chr3:150863600-150863800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:150863600-150863800	Enhancers	Fetal Brain Male	brain
32	chr3:150863600-150863800	Bivalent Enhancer	Placenta	Placenta
33	chr3:150863600-150863800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
34	chr3:150863600-150863800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
35	chr3:150863600-150863800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr3:150863600-150863800	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
37	chr3:150863600-150864000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:150863600-150864000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr3:150863600-150864000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:150863600-150864000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr3:150863600-150864000	Active TSS	Primary B cells from cord blood	blood
42	chr3:150863600-150864000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr3:150863600-150864000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr3:150863600-150864000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:150863600-150864000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr3:150863600-150864000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr3:150863600-150864000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:150863600-150864000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr3:150863600-150864000	Enhancers	Adipose Nuclei	Adipose
50	chr3:150863600-150864000	Bivalent Enhancer	Osteobl	bone

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