Variant report

Variant	rs1471251
Chromosome Location	chr4:87976359-87976360
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:87969835..87971822-chr4:87974907..87977346,2	K562	blood:
2	chr4:87925282..87929320-chr4:87973735..87976929,7	K562	blood:
3	chr4:87969507..87971822-chr4:87975846..87977390,2	K562	blood:
4	chr4:87966822..87969393-chr4:87974722..87976813,3	K562	blood:
5	chr4:87973947..87977443-chr4:87977698..87982276,5	K562	blood:
6	chr4:87925846..87930633-chr4:87974014..87981325,14	K562	blood:
7	chr4:87927611..87929346-chr4:87974999..87977042,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172493	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10516785	0.92[CHD][hapmap];0.89[JPT][hapmap]
rs10516786	0.94[CHD][hapmap];0.94[JPT][hapmap]
rs10516788	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13126334	0.81[CEU][hapmap]
rs17012200	0.92[CHD][hapmap];0.94[JPT][hapmap]
rs17012234	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17604480	0.98[ASN][1000 genomes]
rs17701999	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17752307	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2053770	0.82[CEU][hapmap]
rs340630	0.82[CEU][hapmap]
rs340636	0.82[CEU][hapmap]
rs340641	0.82[CEU][hapmap]
rs375795	0.82[CEU][hapmap]
rs388401	0.82[CEU][hapmap]
rs4693795	0.83[JPT][hapmap]
rs4693798	0.82[CEU][hapmap]
rs4693801	0.86[ASN][1000 genomes]
rs55787557	0.95[ASN][1000 genomes]
rs55816619	0.90[ASN][1000 genomes]
rs55879154	0.84[ASN][1000 genomes]
rs56023922	0.80[ASN][1000 genomes]
rs56050898	0.94[ASN][1000 genomes]
rs56201818	0.95[ASN][1000 genomes]
rs56390363	0.87[ASN][1000 genomes]
rs56395939	0.98[ASN][1000 genomes]
rs56406125	0.87[ASN][1000 genomes]
rs6531948	0.82[CEU][hapmap]
rs6819155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6840258	0.94[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs6854749	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs72667747	0.86[ASN][1000 genomes]
rs72667748	0.86[ASN][1000 genomes]
rs72667750	0.86[ASN][1000 genomes]
rs72667751	0.87[ASN][1000 genomes]
rs72667752	0.87[ASN][1000 genomes]
rs72667753	0.87[ASN][1000 genomes]
rs72667754	0.87[ASN][1000 genomes]
rs72667757	0.94[ASN][1000 genomes]
rs72667759	0.94[ASN][1000 genomes]
rs72667765	0.98[ASN][1000 genomes]
rs7665282	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs767315	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7682652	0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7695426	0.86[ASN][1000 genomes]
rs867196	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009937	chr4:87795314-88008345	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv999176	chr4:87869996-88098136	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv998335	chr4:87869996-88104414	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1001017	chr4:87872160-88087003	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv537166	chr4:87872160-88087003	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv999098	chr4:87899091-88016048	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv537167	chr4:87899091-88016048	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv879525	chr4:87964363-88033352	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1471251	SPARCL1	cis	cerebellum	SCAN
rs1471251	AFF1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87961000-87979200	Weak transcription	HSMMtube	muscle
2	chr4:87963200-87982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:87964600-87995000	Weak transcription	Hela-S3	cervix
4	chr4:87964800-87979200	Weak transcription	A549	lung
5	chr4:87966200-87979200	Weak transcription	NH-A	brain
6	chr4:87968600-87979000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:87968800-87977600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr4:87968800-87978800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:87968800-87979000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:87968800-87979200	Weak transcription	HMEC	breast
11	chr4:87968800-87979200	Weak transcription	HSMM	muscle
12	chr4:87968800-87979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:87968800-87979400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:87968800-87980000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:87968800-87982000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:87968800-87982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr4:87968800-87983400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:87968800-87995000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:87969000-87994600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr4:87970200-87976600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:87970200-87979200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:87970200-87979800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr4:87970200-87989800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr4:87970400-87982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:87970800-87976800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr4:87970800-87977000	Enhancers	Psoas Muscle	Psoas
27	chr4:87970800-87977200	Genic enhancers	Placenta	Placenta
28	chr4:87970800-87978400	Weak transcription	Fetal Brain Male	brain
29	chr4:87971400-87979400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87971800-87976800	Enhancers	Right Atrium	heart
31	chr4:87972000-87976800	Enhancers	Pancreas	Pancrea
32	chr4:87972200-87979800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:87972200-87982200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:87972400-87982200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:87972600-87976400	Weak transcription	Osteobl	bone
36	chr4:87972600-87980400	Weak transcription	Primary T cells from cord blood	blood
37	chr4:87973600-87976800	Enhancers	Brain Cingulate Gyrus	brain
38	chr4:87973800-87976400	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr4:87973800-87977000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr4:87973800-87978600	Enhancers	Brain Hippocampus Middle	brain
41	chr4:87973800-87980200	Enhancers	Liver	Liver
42	chr4:87973800-87980200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr4:87974000-87976800	Enhancers	Brain Angular Gyrus	brain
44	chr4:87974000-87977000	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr4:87974000-87977200	Enhancers	Fetal Heart	heart
46	chr4:87974000-87978400	Enhancers	Brain Substantia Nigra	brain
47	chr4:87974200-87976600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr4:87974200-87976800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
49	chr4:87974200-87977000	Enhancers	Brain Anterior Caudate	brain
50	chr4:87974400-87976800	Enhancers	Aorta	Aorta

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