Variant report

Variant	rs580910
Chromosome Location	chr11:66402333-66402334
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	POLR2A	chr11:66402142-66402609	GM12892	blood:	n/a	n/a
2	POLR2A	chr11:66402131-66402541	GM12878	blood:	n/a	n/a
3	POLR2A	chr11:66401640-66402439	U87	brain:	n/a	n/a
4	POLR2A	chr11:66401812-66402473	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:66402065-66402552	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr11:66401680-66402535	GM12892	blood:	n/a	n/a
7	POLR2A	chr11:66402274-66402404	A549	lung:	n/a	n/a
8	POLR2A	chr11:66402026-66402514	U87	brain:	n/a	n/a
9	POLR2A	chr11:66402090-66402556	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr11:66401711-66402514	U87	brain:	n/a	n/a
11	POLR2A	chr11:66402156-66402545	GM12892	blood:	n/a	n/a
12	POLR2A	chr11:66401575-66402550	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:66399850..66403638-chr11:66403806..66406720,12	K562	blood:
2	chr11:66401664..66404520-chr11:66510709..66512789,2	MCF-7	breast:

Variant related genes	Relation type
RBM4	TF binding region
ENSG00000173715	Chromatin interaction
ENSG00000173933	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12417769	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12577111	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12804382	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12805133	0.91[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs1671062	0.82[JPT][hapmap];0.86[MKK][hapmap]
rs1671063	0.86[MKK][hapmap]
rs1671064	0.80[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs1791684	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1815739	0.80[GIH][hapmap];0.91[JPT][hapmap]
rs2276138	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2279863	0.80[JPT][hapmap]
rs34900764	0.93[EUR][1000 genomes]
rs3741363	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs474602	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs477557	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs486584	0.90[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs4930387	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498045	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs503250	0.83[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs508443	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs509556	0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs535211	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs540874	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs543191	0.83[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs556759	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs560556	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs566673	0.85[CEU][hapmap]
rs569818	0.83[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap]
rs572846	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.80[YRI][hapmap]
rs577023	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577335	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs608248	0.83[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap]
rs618838	0.87[JPT][hapmap];0.83[MEX][hapmap]
rs627330	0.83[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.82[MKK][hapmap]
rs636128	0.80[EUR][1000 genomes]
rs677488	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs678397	0.88[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs682842	0.83[ASW][hapmap];0.82[MKK][hapmap]
rs692892	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs8432	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv897789	chr11:66372390-66634397	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs580910	CCS	cis	multi-tissue	Pritchard
rs580910	CCS	cis	lymphoblastoid	seeQTL
rs580910	PRDX5	cis	cerebellum	SCAN
rs580910	YIF1A	cis	cerebellum	SCAN
rs580910	CCDC85B	cis	parietal	SCAN
rs580910	ACTN3	cis	Muscle Skeletal	GTEx
rs580910	BBS1	cis	cerebellum	SCAN
rs580910	ACTN3	cis	lymphoblastoid	seeQTL
rs580910	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs580910	CDC42EP2	cis	cerebellum	SCAN
rs580910	UNC93B1	cis	cerebellum	SCAN
rs580910	TRMT112	cis	cerebellum	SCAN
rs580910	CTSF	cis	cerebellum	SCAN
rs580910	CTSF	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66385400-66406200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:66386800-66405600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr11:66387000-66403400	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr11:66388600-66402400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr11:66388800-66402400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:66388800-66402400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:66388800-66402400	Strong transcription	Fetal Muscle Leg	muscle
8	chr11:66388800-66402800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:66388800-66403800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:66388800-66404400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr11:66388800-66404800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr11:66389000-66404400	Strong transcription	Fetal Thymus	thymus
13	chr11:66389200-66402400	Strong transcription	Fetal Intestine Large	intestine
14	chr11:66389200-66402800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:66390600-66402600	Strong transcription	K562	blood
16	chr11:66390600-66404800	Strong transcription	Fetal Intestine Small	intestine
17	chr11:66390800-66402600	Strong transcription	A549	lung
18	chr11:66390800-66403200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr11:66391000-66404200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr11:66391200-66402400	Strong transcription	Osteobl	bone
21	chr11:66391200-66403200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr11:66391200-66403800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:66391200-66404400	Strong transcription	Fetal Stomach	stomach
24	chr11:66391200-66404600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:66391600-66404800	Weak transcription	Fetal Brain Male	brain
26	chr11:66391800-66402400	Strong transcription	Liver	Liver
27	chr11:66394200-66405200	Weak transcription	Psoas Muscle	Psoas
28	chr11:66394800-66404800	Weak transcription	Fetal Heart	heart
29	chr11:66395000-66405200	Weak transcription	Small Intestine	intestine
30	chr11:66395400-66405600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:66396600-66405000	Weak transcription	Stomach Mucosa	stomach
32	chr11:66396600-66405600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:66397000-66405000	Weak transcription	Left Ventricle	heart
34	chr11:66397000-66405000	Weak transcription	Right Atrium	heart
35	chr11:66397000-66405000	Weak transcription	Right Ventricle	heart
36	chr11:66397000-66405400	Weak transcription	Esophagus	oesophagus
37	chr11:66397000-66405400	Weak transcription	Pancreas	Pancrea
38	chr11:66397200-66404000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:66397200-66405400	Weak transcription	Aorta	Aorta
40	chr11:66397200-66405400	Weak transcription	Gastric	stomach
41	chr11:66397400-66405000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr11:66397600-66403800	Weak transcription	HepG2	liver
43	chr11:66397600-66404600	Weak transcription	Colonic Mucosa	Colon
44	chr11:66397600-66405200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr11:66397600-66405600	Weak transcription	Ovary	ovary
46	chr11:66397800-66404200	Weak transcription	NHLF	lung
47	chr11:66397800-66405000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:66397800-66405000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:66397800-66405000	Weak transcription	Brain Hippocampus Middle	brain
50	chr11:66397800-66405200	Weak transcription	Brain Anterior Caudate	brain

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