Variant report

Variant	rs6672371
Chromosome Location	chr1:153717182-153717183
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153716694..153719487-chr1:153746319..153748450,2	MCF-7	breast:
2	chr1:153716182..153721431-chr1:153722376..153725586,6	K562	blood:
3	chr1:153714692..153717682-chr1:153721642..153723876,3	K562	blood:
4	chr1:153700874..153704852-chr1:153714876..153719241,5	MCF-7	breast:
5	chr1:153638167..153640842-chr1:153716743..153718282,2	K562	blood:
6	chr1:153716864..153718651-chr1:153718917..153721137,2	K562	blood:

Variant related genes	Relation type
ENSG00000243613	Chromatin interaction
ENSG00000143554	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000233222	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10082235	1.00[CHB][hapmap]
rs11264299	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264336	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1132619	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12062022	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12068901	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12070179	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12070559	0.92[EUR][1000 genomes]
rs12071801	0.92[EUR][1000 genomes]
rs12076697	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12097043	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12097583	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2318436	1.00[ASN][1000 genomes]
rs28730729	1.00[ASN][1000 genomes]
rs28730731	1.00[ASN][1000 genomes]
rs35240348	1.00[ASN][1000 genomes]
rs36064263	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3891075	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4073768	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41265168	1.00[ASN][1000 genomes]
rs41265191	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4845359	1.00[ASN][1000 genomes]
rs55658698	0.86[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778008	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56167936	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56910871	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57314764	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57482283	1.00[ASN][1000 genomes]
rs60100741	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60316596	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60827720	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61803563	0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803565	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803566	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803567	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803571	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61803573	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61805738	1.00[ASN][1000 genomes]
rs61806710	1.00[ASN][1000 genomes]
rs61806714	1.00[ASN][1000 genomes]
rs61806719	1.00[ASN][1000 genomes]
rs6427085	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660232	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6663011	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6663988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668229	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682411	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6687602	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6689176	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692298	1.00[CHB][hapmap]
rs74115713	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7512561	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515716	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520045	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7520235	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533987	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7536700	1.00[CHB][hapmap]
rs7543790	1.00[CHB][hapmap]
rs7556155	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556379	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556575	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8532	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
12	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
13	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
16	nsv1002328	chr1:153672031-153718746	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
18	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6672371	SLC27A3	Cis_1M	lymphoblastoid	RTeQTL
rs6672371	S100A13	cis	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153703600-153718200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:153704000-153719600	Weak transcription	Fetal Heart	heart
3	chr1:153707200-153730400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:153707600-153722200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:153711400-153718600	Strong transcription	Fetal Stomach	stomach
6	chr1:153711400-153735600	Strong transcription	Fetal Muscle Leg	muscle
7	chr1:153711600-153721400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:153712400-153719600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:153712600-153721800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:153712600-153721800	Strong transcription	Brain Anterior Caudate	brain
11	chr1:153712600-153722400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:153712600-153741400	Strong transcription	Placenta	Placenta
13	chr1:153712800-153717200	Strong transcription	Brain Substantia Nigra	brain
14	chr1:153712800-153717600	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr1:153712800-153720200	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:153712800-153720400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr1:153712800-153721800	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr1:153712800-153721800	Strong transcription	Colon Smooth Muscle	Colon
19	chr1:153712800-153725600	Strong transcription	Fetal Lung	lung
20	chr1:153712800-153737800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr1:153712800-153737800	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr1:153712800-153738000	Strong transcription	Fetal Brain Female	brain
23	chr1:153712800-153738200	Strong transcription	Thymus	Thymus
24	chr1:153712800-153742800	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:153712800-153743200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:153712800-153744800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:153712800-153746400	Strong transcription	Brain Germinal Matrix	brain
28	chr1:153712800-153751800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:153713000-153717400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr1:153713000-153717400	Genic enhancers	Fetal Kidney	kidney
31	chr1:153713000-153717400	Strong transcription	K562	blood
32	chr1:153713000-153720400	Strong transcription	Left Ventricle	heart
33	chr1:153713000-153721400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:153713000-153721400	Strong transcription	Brain Cingulate Gyrus	brain
35	chr1:153713000-153721400	Strong transcription	Hela-S3	cervix
36	chr1:153713000-153721800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:153713000-153721800	Strong transcription	Adipose Nuclei	Adipose
38	chr1:153713000-153721800	Strong transcription	Brain Hippocampus Middle	brain
39	chr1:153713000-153722000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr1:153713000-153725600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr1:153713000-153728600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:153713000-153734800	Strong transcription	Spleen	Spleen
43	chr1:153713000-153735200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:153713000-153738200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:153713000-153738600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:153713000-153745400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:153713000-153745400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:153713000-153746400	Strong transcription	Primary T cells from cord blood	blood
49	chr1:153713000-153747000	Strong transcription	Dnd41	blood
50	chr1:153713200-153717200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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