Variant report

Variant	rs3778515
Chromosome Location	chr6:57042709-57042710
allele	A/C
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	POLR2A	chr6:57042561-57042832	K562	blood:	n/a	n/a
2	POLR2A	chr6:57042435-57046203	K562	blood:	n/a	n/a
3	POLR2A	chr6:57042396-57042981	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:57037434..57039055-chr6:57042704..57045228,2	MCF-7	breast:
2	chr6:57041061..57044747-chr6:57049624..57053338,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226803	TF binding region
ENSG00000226803	Chromatin interaction
ENSG00000112208	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1157713	0.87[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190416	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12190434	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12192711	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210597	0.96[ASN][1000 genomes]
rs12211611	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs2100305	0.80[ASN][1000 genomes]
rs2273921	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734738	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800019	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.81[MEX][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3996929	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3996933	0.80[ASN][1000 genomes]
rs3996937	0.82[ASN][1000 genomes]
rs4715646	0.80[ASN][1000 genomes]
rs6459180	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6913707	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6926980	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6928715	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6929783	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6936472	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7743855	0.86[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7744316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[ASN][1000 genomes]
rs7744824	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753537	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7753927	0.87[ASW][hapmap];0.86[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.80[ASN][1000 genomes]
rs7763570	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180538	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9349843	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9367704	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9367708	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9370564	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370565	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9382689	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396259	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952647	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9885757	0.93[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3430228	chr6:56830972-57079281	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers 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	nsv462949	chr6:56973902-57098973	ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv603190	chr6:56973902-57098973	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3778515	KIAA1586	Cis_1M	lymphoblastoid	RTeQTL
rs3778515	RAB23	cis	cerebellum	SCAN
rs3778515	ZNF451	cis	cerebellum	SCAN
rs3778515	BEND6	cis	cerebellum	SCAN
rs3778515	RAB23	Cis_1M	lymphoblastoid	RTeQTL
rs3778515	BEND6	cis	parietal	SCAN
rs3778515	BEND6	cis	Muscle Skeletal	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57038000-57054200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:57038000-57056000	Weak transcription	Spleen	Spleen
3	chr6:57038000-57081600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:57038200-57051200	Weak transcription	Small Intestine	intestine
5	chr6:57038200-57063800	Weak transcription	Esophagus	oesophagus
6	chr6:57038200-57063800	Weak transcription	Gastric	stomach
7	chr6:57038400-57047000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:57038400-57056200	Weak transcription	Brain Germinal Matrix	brain
9	chr6:57038400-57072800	Weak transcription	Pancreas	Pancrea
10	chr6:57038400-57079600	Weak transcription	Fetal Brain Female	brain
11	chr6:57038600-57047000	Weak transcription	Brain Anterior Caudate	brain
12	chr6:57038600-57047600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:57038600-57049800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:57038600-57064000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:57038800-57047600	Weak transcription	Primary B cells from cord blood	blood
16	chr6:57038800-57047600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr6:57038800-57047800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:57038800-57048000	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:57038800-57056400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:57038800-57060400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr6:57039000-57047800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:57039000-57047800	Weak transcription	Lung	lung
23	chr6:57039000-57049400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:57039000-57050000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:57039000-57056400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:57039000-57086000	Weak transcription	Thymus	Thymus
27	chr6:57039200-57045600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:57039200-57045800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr6:57039200-57046600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:57039200-57046800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:57039200-57046800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr6:57039200-57046800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr6:57039200-57046800	Weak transcription	Liver	Liver
34	chr6:57039200-57046800	Weak transcription	Fetal Thymus	thymus
35	chr6:57039200-57047400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:57039200-57047600	Weak transcription	Primary T cells from cord blood	blood
37	chr6:57039200-57047600	Weak transcription	Brain Hippocampus Middle	brain
38	chr6:57039200-57047800	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:57039200-57047800	Weak transcription	Fetal Intestine Large	intestine
40	chr6:57039200-57047800	Weak transcription	Fetal Kidney	kidney
41	chr6:57039200-57047800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr6:57039200-57054200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:57039200-57056200	Weak transcription	Fetal Intestine Small	intestine
44	chr6:57039400-57043200	Weak transcription	HMEC	breast
45	chr6:57039400-57046600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:57039400-57046800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr6:57039400-57047000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:57039400-57047800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:57039400-57047800	Weak transcription	HUVEC	blood vessel
50	chr6:57039400-57048000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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