Variant report

Variant	rs3800503
Chromosome Location	chr6:13619629-13619630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13619286-13619783	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:13618693-13627590	K562	blood:	n/a	n/a
3	POLR2A	chr6:13619285-13619739	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:13619297-13619916	GM12878	blood:	n/a	n/a
5	POLR2A	chr6:13618688-13619730	K562	blood:	n/a	n/a
6	POLR2A	chr6:13618631-13619885	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr6:13619343-13619781	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:13619205-13620096	HepG2	liver:	n/a	n/a
9	POLR2A	chr6:13619494-13620027	K562	blood:	n/a	n/a
10	POLR2A	chr6:13619256-13619863	MCF-7	breast:	n/a	n/a
11	POLR2A	chr6:13619281-13619813	HepG2	liver:	n/a	n/a
12	POLR2A	chr6:13619485-13619885	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:13618690-13619818	K562	blood:	n/a	n/a
14	POLR2A	chr6:13619178-13619787	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13617821..13621321-chr6:13710420..13713075,4	MCF-7	breast:
2	chr6:13614163..13617329-chr6:13617495..13621513,6	MCF-7	breast:
3	chr6:13617283..13619910-chr6:13629939..13633693,3	K562	blood:
4	chr6:13574031..13576130-chr6:13618048..13620818,3	K562	blood:
5	chr6:13617485..13620464-chr6:13688462..13691344,2	K562	blood:
6	chr6:13619203..13621025-chr6:13638291..13640853,2	K562	blood:
7	chr6:13617338..13618860-chr6:13619062..13621031,2	MCF-7	breast:
8	chr6:13618139..13620523-chr6:13661080..13663050,2	K562	blood:
9	chr6:13572897..13576165-chr6:13619318..13622919,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000261071	TF binding region
ENSG00000261071	Chromatin interaction
ENSG00000225921	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000010017	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10807467	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10948804	1.00[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10948811	0.92[YRI][hapmap]
rs11962124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12209803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664567	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1362520	0.85[YRI][hapmap]
rs1573702	0.93[YRI][hapmap]
rs2237092	0.89[YRI][hapmap]
rs2841514	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2841515	0.96[CEU][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2841517	0.94[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2841518	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2841520	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2841521	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2841522	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2841523	0.96[CEU][hapmap];0.98[GIH][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2841524	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3757260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823453	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3846912	0.89[YRI][hapmap]
rs3906327	0.93[YRI][hapmap]
rs6459020	0.93[YRI][hapmap]
rs6899402	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6915775	0.85[YRI][hapmap]
rs6940759	0.93[YRI][hapmap]
rs7744218	0.93[YRI][hapmap]
rs7745101	0.88[EUR][1000 genomes]
rs7760411	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]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3800503	RANBP9	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13616600-13624200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:13616600-13637400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:13617000-13619800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:13617000-13622800	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr6:13617000-13628200	Strong transcription	Fetal Muscle Leg	muscle
6	chr6:13617000-13633000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr6:13617200-13620800	Strong transcription	Spleen	Spleen
8	chr6:13617200-13622800	Strong transcription	Fetal Kidney	kidney
9	chr6:13617200-13623400	Strong transcription	Fetal Stomach	stomach
10	chr6:13617200-13623600	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr6:13617200-13623800	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr6:13617200-13624000	Strong transcription	Brain Anterior Caudate	brain
13	chr6:13617200-13624600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:13617200-13625000	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:13617200-13626000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr6:13617200-13627200	Strong transcription	NH-A	brain
17	chr6:13617200-13627600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:13617200-13632800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr6:13617200-13632800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr6:13617200-13633800	Weak transcription	Stomach Mucosa	stomach
21	chr6:13617200-13634600	Strong transcription	Placenta	Placenta
22	chr6:13617200-13634800	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr6:13617200-13634800	Strong transcription	Fetal Intestine Large	intestine
24	chr6:13617200-13638800	Weak transcription	Aorta	Aorta
25	chr6:13617400-13620400	Strong transcription	Gastric	stomach
26	chr6:13617400-13620400	Strong transcription	Pancreas	Pancrea
27	chr6:13617400-13622200	Strong transcription	Right Ventricle	heart
28	chr6:13617400-13622800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr6:13617400-13622800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
30	chr6:13617400-13625400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:13617400-13625400	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:13617400-13625600	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr6:13617400-13627600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr6:13617400-13627600	Strong transcription	HSMMtube	muscle
35	chr6:13617400-13630400	Strong transcription	Primary B cells from cord blood	blood
36	chr6:13617400-13636400	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:13617600-13620000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:13617600-13623000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:13617600-13624000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:13617600-13626000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:13617600-13626000	Strong transcription	NHEK	skin
42	chr6:13617600-13627000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:13617600-13627400	Strong transcription	Left Ventricle	heart
44	chr6:13617600-13627600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:13617600-13627800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr6:13617600-13632000	Strong transcription	Adipose Nuclei	Adipose
47	chr6:13617600-13632800	Strong transcription	Primary hematopoietic stem cells	blood
48	chr6:13617600-13633000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr6:13617600-13634600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:13617600-13634800	Strong transcription	Primary T cells from cord blood	blood

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