Variant report

Variant	rs7760411
Chromosome Location	chr6:13628059-13628060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13622285..13628716-chr6:13632838..13638490,8	K562	blood:
2	chr6:13627462..13629915-chr6:13630026..13632119,2	K562	blood:
3	chr6:13619174..13622491-chr6:13623687..13628179,5	MCF-7	breast:
4	chr6:13626339..13628335-chr6:13647622..13649299,2	K562	blood:
5	chr6:13624828..13628073-chr6:13628586..13632112,4	K562	blood:

Variant related genes	Relation type
ENSG00000010017	Chromatin interaction
ENSG00000268059	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10807467	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10948804	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11962124	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12209803	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12664567	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2253217	0.84[YRI][hapmap]
rs2841514	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2841515	0.87[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841517	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841518	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2841520	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2841521	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2841522	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2841523	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2841524	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757260	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3800503	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3823453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6899402	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745101	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1016744	chr6:13622143-13664028	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1019422	chr6:13622143-13694781	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7760411	RANBP9	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13616600-13637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:13617000-13628200	Strong transcription	Fetal Muscle Leg	muscle
3	chr6:13617000-13633000	Strong transcription	Fetal Muscle Trunk	muscle
4	chr6:13617200-13632800	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr6:13617200-13632800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr6:13617200-13633800	Weak transcription	Stomach Mucosa	stomach
7	chr6:13617200-13634600	Strong transcription	Placenta	Placenta
8	chr6:13617200-13634800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:13617200-13634800	Strong transcription	Fetal Intestine Large	intestine
10	chr6:13617200-13638800	Weak transcription	Aorta	Aorta
11	chr6:13617400-13630400	Strong transcription	Primary B cells from cord blood	blood
12	chr6:13617400-13636400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:13617600-13632000	Strong transcription	Adipose Nuclei	Adipose
14	chr6:13617600-13632800	Strong transcription	Primary hematopoietic stem cells	blood
15	chr6:13617600-13633000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:13617600-13634600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:13617600-13634800	Strong transcription	Primary T cells from cord blood	blood
18	chr6:13617600-13635400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr6:13617600-13642200	Strong transcription	Fetal Thymus	thymus
20	chr6:13617600-13642200	Strong transcription	HSMM	muscle
21	chr6:13617600-13642400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:13617800-13628600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:13617800-13628600	Strong transcription	HMEC	breast
24	chr6:13617800-13629600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:13617800-13630000	Strong transcription	NHDF-Ad	bronchial
26	chr6:13617800-13632400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr6:13617800-13632600	Strong transcription	Liver	Liver
28	chr6:13617800-13633000	Strong transcription	Duodenum Mucosa	Duodenum
29	chr6:13617800-13633200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr6:13617800-13634800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr6:13617800-13638400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:13618000-13630000	Strong transcription	GM12878-XiMat	blood
33	chr6:13618000-13632200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:13618000-13633000	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:13618000-13633200	Strong transcription	Osteobl	bone
36	chr6:13618000-13634800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:13618000-13634800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:13618000-13635400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:13618000-13641200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr6:13618000-13644200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr6:13618200-13629600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:13618200-13632800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:13618200-13635400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr6:13618200-13641800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:13618200-13644400	Strong transcription	K562	blood
46	chr6:13618200-13661200	Weak transcription	Fetal Brain Male	brain
47	chr6:13618800-13632200	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr6:13619800-13631600	Weak transcription	Psoas Muscle	Psoas
49	chr6:13620000-13632200	Weak transcription	Fetal Heart	heart
50	chr6:13620000-13647200	Strong transcription	Dnd41	blood

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