Variant report

Variant	rs6455371
Chromosome Location	chr6:71273253-71273254
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr6:71273251-71273565	H1-hESC	embryonic stem cell:	n/a	n/a
2	KAP1	chr6:71273221-71273711	U2OS	brain:	n/a	n/a
3	SP1	chr6:71273170-71273685	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:71268001..71269667-chr6:71271923..71274246,2	K562	blood:

Variant related genes	Relation type
C6orf57	TF binding region

Extended variants
information (count: 161 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:154)

rs_ID	r²[population]
rs10485118	1.00[JPT][hapmap]
rs10485119	1.00[JPT][hapmap]
rs1048886	0.92[JPT][hapmap]
rs1075262	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.82[ASN][1000 genomes]
rs1075263	1.00[JPT][hapmap]
rs10945230	1.00[JPT][hapmap]
rs10945236	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1140297	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11965656	1.00[JPT][hapmap]
rs1208475	0.85[YRI][hapmap]
rs1208476	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]
rs1208477	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12190556	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12197942	1.00[JPT][hapmap]
rs12197963	1.00[JPT][hapmap]
rs12198920	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12203298	1.00[JPT][hapmap]
rs12205103	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12209965	1.00[JPT][hapmap]
rs12215765	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][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]
rs13199529	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13202450	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13206086	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213357	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13437371	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13654	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[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];0.88[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[EUR][1000 genomes]
rs1917344	0.91[AMR][1000 genomes];0.90[EUR][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	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2639297	1.00[JPT][hapmap]
rs2691505	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2747702	1.00[JPT][hapmap]
rs2747703	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28360504	0.84[ASN][1000 genomes]
rs2842063	0.92[JPT][hapmap]
rs3193656	1.00[JPT][hapmap]
rs34378057	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34710086	0.82[ASN][1000 genomes]
rs34873840	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35516318	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35542509	0.93[ASN][1000 genomes]
rs3736751	1.00[JPT][hapmap]
rs3736752	0.92[JPT][hapmap]
rs3763251	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3846746	0.92[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]
rs57836066	0.82[ASN][1000 genomes]
rs62421394	0.84[ASN][1000 genomes]
rs6455367	1.00[JPT][hapmap]
rs6455370	1.00[JPT][hapmap]
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];0.88[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	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6925839	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[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	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7739098	1.00[CEU][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[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	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[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];0.88[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];0.88[YRI][hapmap]
rs9294876	1.00[JPT][hapmap]
rs9446245	1.00[JPT][hapmap]
rs9446248	1.00[JPT][hapmap]
rs9446267	1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes]
rs9446271	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9446274	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9446275	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9455092	1.00[JPT][hapmap]
rs9455104	1.00[JPT][hapmap]
rs9455105	1.00[JPT][hapmap]
rs9455113	1.00[JPT][hapmap]
rs9455121	1.00[JPT][hapmap]
rs9455130	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs9455132	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs9455133	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	0.91[JPT][hapmap]
rs9455173	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9455179	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9455180	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9455185	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9455186	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
3	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
4	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
5	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
6	nsv886146	chr6:71219464-71317480	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6455371	C6orf57	cis	lung	GTEx
rs6455371	C6orf57	cis	cerebellum	SCAN
rs6455371	C6orf57	cis	Thyroid	GTEx
rs6455371	C6orf57	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71214000-71276000	Weak transcription	Brain Angular Gyrus	brain
2	chr6:71214000-71276000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:71214000-71276000	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:71214600-71276000	Weak transcription	A549	lung
5	chr6:71228600-71276000	Weak transcription	Primary T cells from cord blood	blood
6	chr6:71229600-71276200	Weak transcription	Aorta	Aorta
7	chr6:71237000-71276200	Weak transcription	Left Ventricle	heart
8	chr6:71243400-71276200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:71245400-71276400	Weak transcription	Esophagus	oesophagus
10	chr6:71245400-71276400	Weak transcription	Gastric	stomach
11	chr6:71245600-71276200	Weak transcription	Primary B cells from cord blood	blood
12	chr6:71249200-71275800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:71249400-71276200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:71249800-71276200	Weak transcription	Fetal Brain Female	brain
15	chr6:71250000-71273400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:71250000-71274600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:71250000-71276000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:71250000-71276000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:71250400-71276000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:71250600-71276000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr6:71250600-71276000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:71250600-71276200	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:71251800-71276200	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr6:71253400-71276200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:71257600-71274200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:71260000-71275200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:71260000-71276000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr6:71260400-71275800	Weak transcription	Fetal Intestine Large	intestine
29	chr6:71260400-71276000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:71260600-71276000	Weak transcription	Primary hematopoietic stem cells	blood
31	chr6:71260800-71275800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr6:71267400-71276000	Weak transcription	Liver	Liver
33	chr6:71268200-71276000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr6:71268200-71276000	Weak transcription	Lung	lung
35	chr6:71268200-71276200	Weak transcription	Placenta	Placenta
36	chr6:71268400-71276000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:71268600-71275800	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:71268600-71276000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr6:71268600-71276200	Weak transcription	Ovary	ovary
40	chr6:71269000-71275600	Weak transcription	Fetal Intestine Small	intestine
41	chr6:71269000-71276000	Weak transcription	Fetal Stomach	stomach
42	chr6:71269000-71276000	Weak transcription	Pancreas	Pancrea
43	chr6:71270400-71276000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr6:71270800-71276000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:71270800-71276200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr6:71271800-71276000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr6:71272000-71274600	Weak transcription	Fetal Lung	lung
48	chr6:71272400-71274400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr6:71272600-71276000	Enhancers	Adipose Nuclei	Adipose
50	chr6:71272800-71273600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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