Variant report

Variant	rs17216685
Chromosome Location	chr3:56647799-56647800
allele	C/T
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	chr3:56647766-56647836	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr3:56647783-56647983	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56647300..56648856-chr3:56648916..56651486,2	K562	blood:

Variant related genes	Relation type
CCDC66	TF binding region
ENSG00000180376	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10212341	0.89[CHD][hapmap]
rs10222629	0.84[ASN][1000 genomes]
rs11130525	0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs11130526	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs11130527	0.85[JPT][hapmap]
rs11719707	0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.84[ASN][1000 genomes]
rs11719726	0.84[ASN][1000 genomes]
rs12631156	0.81[AMR][1000 genomes]
rs1316647	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs13317989	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.81[ASN][1000 genomes]
rs1388256	0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2291498	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs2291500	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2317132	0.88[ASN][1000 genomes]
rs282525	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282530	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282531	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282532	0.81[AMR][1000 genomes]
rs282534	0.82[AMR][1000 genomes]
rs282538	0.81[AMR][1000 genomes]
rs282542	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs282543	0.81[AMR][1000 genomes]
rs3172355	0.94[ASW][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3732505	0.94[ASW][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4681726	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs4681903	0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4681904	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4681937	0.84[ASN][1000 genomes]
rs4681955	0.84[ASN][1000 genomes]
rs4682001	0.84[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs4974221	0.82[AMR][1000 genomes]
rs4974223	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55742226	0.84[ASN][1000 genomes]
rs56263252	0.84[ASN][1000 genomes]
rs6445811	0.84[ASN][1000 genomes]
rs6445812	0.84[ASN][1000 genomes]
rs6556	0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6767903	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6794450	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6799086	0.80[ASN][1000 genomes]
rs7612464	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs7628343	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7633478	0.83[ASN][1000 genomes]
rs7649872	0.84[ASN][1000 genomes]
rs9311609	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.84[ASN][1000 genomes]
rs953540	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9809117	0.83[ASN][1000 genomes]
rs9814014	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9816100	0.84[ASN][1000 genomes]
rs9816265	0.84[ASN][1000 genomes]
rs9819952	0.84[ASN][1000 genomes]
rs9822876	0.81[JPT][hapmap]
rs9826788	0.83[ASN][1000 genomes]
rs9830377	0.81[ASN][1000 genomes]
rs9834239	0.82[ASN][1000 genomes]
rs9841851	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9847362	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.83[ASN][1000 genomes]
rs9864701	0.84[ASN][1000 genomes]
rs9867302	0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs9868059	0.84[ASN][1000 genomes]
rs9871265	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs9872059	0.86[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs9881152	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9883842	0.84[ASN][1000 genomes]
rs9985317	0.81[AMR][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	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17216685	FLNB	cis	cerebellum	SCAN
rs17216685	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs17216685	LOC285331	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56603200-56650400	Weak transcription	K562	blood
2	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
3	chr3:56607800-56650200	Weak transcription	Psoas Muscle	Psoas
4	chr3:56625200-56650400	Weak transcription	NHEK	skin
5	chr3:56625200-56653400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:56626400-56656200	Weak transcription	Stomach Mucosa	stomach
7	chr3:56628600-56649600	Weak transcription	HepG2	liver
8	chr3:56629000-56648000	Weak transcription	NH-A	brain
9	chr3:56629600-56648200	Weak transcription	NHDF-Ad	bronchial
10	chr3:56630000-56654400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:56633800-56647800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:56634000-56651400	Weak transcription	Fetal Brain Male	brain
13	chr3:56640000-56650000	Weak transcription	HMEC	breast
14	chr3:56640400-56650800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:56640600-56647800	Weak transcription	GM12878-XiMat	blood
16	chr3:56640600-56650400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:56640600-56652600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:56640800-56647800	Weak transcription	Dnd41	blood
19	chr3:56640800-56649400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:56640800-56649400	Weak transcription	Osteobl	bone
21	chr3:56640800-56649800	Weak transcription	Fetal Kidney	kidney
22	chr3:56640800-56650400	Weak transcription	NHLF	lung
23	chr3:56640800-56650600	Weak transcription	HSMMtube	muscle
24	chr3:56640800-56650800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:56640800-56664200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:56640800-56695400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:56643000-56649400	Strong transcription	Primary B cells from cord blood	blood
29	chr3:56644200-56664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:56644400-56647800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:56644400-56652000	Strong transcription	Fetal Lung	lung
32	chr3:56644400-56686400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:56644600-56647800	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr3:56644600-56655800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:56644600-56665600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:56644600-56668600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:56644800-56648200	Strong transcription	Fetal Stomach	stomach
38	chr3:56644800-56648400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr3:56644800-56648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:56644800-56649600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:56644800-56649600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:56644800-56655400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:56644800-56656000	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:56644800-56669800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr3:56644800-56708200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr3:56645000-56648200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:56645000-56650600	Weak transcription	A549	lung
48	chr3:56645000-56650800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr3:56645200-56651600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr3:56645200-56657000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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