Variant report

Variant	rs1208476
Chromosome Location	chr6:71152462-71152463
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:71122917..71125133-chr6:71152387..71154876,3	K562	blood:
2	chr6:71103846..71108205-chr6:71146904..71152814,7	K562	blood:
3	chr6:71145846..71148464-chr6:71150889..71153537,5	K562	blood:
4	chr6:71145846..71148176-chr6:71151672..71153537,2	K562	blood:
5	chr6:71121778..71124489-chr6:71152235..71154710,3	K562	blood:

Variant related genes	Relation type
ENSG00000224349	Chromatin interaction
ENSG00000237643	Chromatin interaction
ENSG00000082269	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10485118	1.00[JPT][hapmap]
rs10485119	1.00[JPT][hapmap]
rs1048886	0.92[JPT][hapmap]
rs1075262	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1075263	1.00[JPT][hapmap]
rs10945230	1.00[JPT][hapmap]
rs10945236	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11965656	1.00[JPT][hapmap]
rs1208477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12190556	0.96[CEU][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs12197942	1.00[JPT][hapmap]
rs12197963	1.00[JPT][hapmap]
rs12198920	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12203298	1.00[JPT][hapmap]
rs12209965	1.00[JPT][hapmap]
rs12215765	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12216376	1.00[JPT][hapmap]
rs12526164	1.00[JPT][hapmap]
rs12526827	1.00[JPT][hapmap]
rs12527634	1.00[JPT][hapmap]
rs12529284	1.00[JPT][hapmap]
rs13202450	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13206086	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13654	0.81[EUR][1000 genomes]
rs16869156	1.00[JPT][hapmap]
rs16869158	1.00[JPT][hapmap]
rs16869170	1.00[JPT][hapmap]
rs16869211	0.92[JPT][hapmap]
rs16869221	1.00[JPT][hapmap]
rs16869228	1.00[JPT][hapmap]
rs16869238	1.00[JPT][hapmap]
rs16869243	1.00[JPT][hapmap]
rs16869244	0.92[JPT][hapmap]
rs16869267	1.00[JPT][hapmap]
rs16869273	1.00[JPT][hapmap]
rs16869338	1.00[JPT][hapmap]
rs16869353	1.00[JPT][hapmap]
rs16869370	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs16869371	1.00[JPT][hapmap]
rs16869373	1.00[JPT][hapmap]
rs16880770	1.00[JPT][hapmap]
rs1739338	1.00[JPT][hapmap]
rs1775338	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2207423	1.00[JPT][hapmap]
rs2273210	1.00[JPT][hapmap]
rs2293297	1.00[JPT][hapmap]
rs2295200	1.00[JPT][hapmap]
rs2346889	1.00[JPT][hapmap]
rs2346890	1.00[JPT][hapmap]
rs2347427	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2639297	1.00[JPT][hapmap]
rs2747702	1.00[JPT][hapmap]
rs2747703	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842063	0.92[JPT][hapmap]
rs3193656	1.00[JPT][hapmap]
rs34378057	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34873840	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35516318	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35542509	0.81[ASN][1000 genomes]
rs3736751	1.00[JPT][hapmap]
rs3736752	0.92[JPT][hapmap]
rs3763251	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3846746	0.93[JPT][hapmap]
rs3846748	1.00[JPT][hapmap]
rs3846750	1.00[JPT][hapmap]
rs3889007	1.00[JPT][hapmap]
rs4283855	1.00[JPT][hapmap]
rs4496758	1.00[JPT][hapmap]
rs6455367	1.00[JPT][hapmap]
rs6455370	1.00[JPT][hapmap]
rs6455371	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6900840	1.00[JPT][hapmap]
rs6902797	1.00[JPT][hapmap]
rs6902986	1.00[JPT][hapmap]
rs6906572	1.00[JPT][hapmap]
rs6906592	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs6910903	1.00[JPT][hapmap]
rs6911812	1.00[JPT][hapmap]
rs6911983	1.00[JPT][hapmap]
rs6913548	1.00[JPT][hapmap]
rs6915405	1.00[JPT][hapmap]
rs6916974	1.00[JPT][hapmap]
rs6917368	1.00[JPT][hapmap]
rs6918393	0.92[JPT][hapmap]
rs6922680	1.00[JPT][hapmap]
rs6925112	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6926591	1.00[JPT][hapmap]
rs6930397	1.00[JPT][hapmap]
rs6931901	1.00[JPT][hapmap]
rs6933150	1.00[JPT][hapmap]
rs6933784	1.00[JPT][hapmap]
rs6939478	1.00[JPT][hapmap]
rs6939814	1.00[JPT][hapmap]
rs6940416	1.00[JPT][hapmap]
rs6941205	0.92[JPT][hapmap]
rs6942012	1.00[JPT][hapmap]
rs7341224	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7739098	0.96[CEU][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7740873	1.00[JPT][hapmap]
rs7741265	1.00[JPT][hapmap]
rs7743819	1.00[JPT][hapmap]
rs7752409	1.00[JPT][hapmap]
rs7753355	1.00[JPT][hapmap]
rs7756652	0.82[EUR][1000 genomes]
rs7757026	1.00[JPT][hapmap]
rs7759464	1.00[JPT][hapmap]
rs7765110	1.00[JPT][hapmap]
rs7766075	1.00[JPT][hapmap]
rs7767109	1.00[JPT][hapmap]
rs7769582	1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7775962	1.00[JPT][hapmap]
rs9283835	1.00[JPT][hapmap]
rs9294868	1.00[JPT][hapmap]
rs9294872	1.00[JPT][hapmap]
rs9294874	1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[ASN][1000 genomes]
rs9294876	1.00[JPT][hapmap]
rs9446245	1.00[JPT][hapmap]
rs9446248	1.00[JPT][hapmap]
rs9446267	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9446274	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9446275	0.81[AMR][1000 genomes]
rs9455092	1.00[JPT][hapmap]
rs9455104	1.00[JPT][hapmap]
rs9455105	1.00[JPT][hapmap]
rs9455106	0.84[YRI][hapmap]
rs9455113	1.00[JPT][hapmap]
rs9455121	1.00[JPT][hapmap]
rs9455125	0.85[YRI][hapmap]
rs9455130	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9455132	1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9455133	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9455158	0.92[JPT][hapmap]
rs9455160	1.00[JPT][hapmap]
rs9455162	1.00[JPT][hapmap]
rs9455163	1.00[JPT][hapmap]
rs9455167	0.91[JPT][hapmap]
rs9455168	0.92[JPT][hapmap]
rs9455179	0.80[AMR][1000 genomes]
rs9455180	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9455185	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9455186	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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
2	nsv886142	chr6:70741209-71251421	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1026229	chr6:71016272-71183503	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv886144	chr6:71018467-71214201	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv886145	chr6:71119524-71317480	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1208476	C6orf57	cis	Thyroid	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71124000-71157600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:71124200-71154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:71124200-71157800	Weak transcription	Spleen	Spleen
4	chr6:71124200-71159800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:71124400-71152800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:71124400-71159800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:71124400-71160400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:71124400-71192800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:71124600-71157200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:71124600-71157800	Weak transcription	Colonic Mucosa	Colon
11	chr6:71125400-71188800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:71125400-71188800	Weak transcription	HSMM	muscle
13	chr6:71125600-71162400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:71126000-71157800	Weak transcription	Dnd41	blood
15	chr6:71128600-71156800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr6:71128800-71154800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr6:71128800-71157800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:71130200-71183200	Weak transcription	Brain Angular Gyrus	brain
19	chr6:71130200-71185400	Weak transcription	K562	blood
20	chr6:71134000-71213400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:71134200-71161400	Weak transcription	Small Intestine	intestine
22	chr6:71136600-71157200	Weak transcription	Brain Hippocampus Middle	brain
23	chr6:71136600-71157800	Weak transcription	Pancreas	Pancrea
24	chr6:71136800-71154800	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr6:71136800-71157600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr6:71136800-71157800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:71136800-71213600	Weak transcription	Brain Substantia Nigra	brain
28	chr6:71137400-71154400	Weak transcription	HMEC	breast
29	chr6:71139400-71157800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr6:71139400-71159800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:71140400-71157800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:71140600-71158000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:71141000-71159200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:71141200-71157600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:71141200-71159600	Weak transcription	Primary T cells from cord blood	blood
36	chr6:71141400-71152600	Weak transcription	HepG2	liver
37	chr6:71141400-71153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:71141400-71154000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:71141400-71154600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr6:71141400-71157800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:71141400-71157800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:71141400-71157800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:71141400-71158000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:71141400-71158000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr6:71141400-71158000	Weak transcription	NHEK	skin
46	chr6:71141400-71160000	Weak transcription	Gastric	stomach
47	chr6:71141400-71183400	Weak transcription	Right Ventricle	heart
48	chr6:71141400-71186800	Weak transcription	Fetal Brain Female	brain
49	chr6:71142000-71153000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr6:71142400-71157200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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