Variant report

Variant	rs10936201
Chromosome Location	chr3:160121839-160121840
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr3:160121706-160122093	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr3:160121790-160122144	K562	blood:	n/a	n/a
3	WRNIP1	chr3:160121793-160121951	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:160121013-160123358	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:160121821-160121871	AG04450	lung:	fetal
2	chr3:160121821-160121871	HL-60	blood:	n/a
3	chr3:160121821-160121871	ovcar-3	ovarian:	n/a
4	chr3:160121821-160121871	AG09309	skin:	n/a
5	chr3:160121821-160121871	HCF	heart:	n/a
6	chr3:160121821-160121871	HRPEpiC	eye:	n/a
7	chr3:160121821-160121871	MCF-7	breast:	n/a
8	chr3:160121821-160121871	K562	blood:	n/a
9	chr3:160121821-160121871	T-47D	breast:	n/a
10	chr3:160121821-160121871	CMK	blood:	n/a
11	chr3:160121821-160121871	NH-A	brain:	n/a
12	chr3:160121821-160121871	Caco-2	colon:	n/a
13	chr3:160121821-160121871	MCF10A-Er-Src	breast:	n/a
14	chr3:160121821-160121871	ProgFib	skin:	n/a
15	chr3:160121821-160121871	HEEpiC	esophagus:	n/a
16	chr3:160121821-160121871	HMEC	breast:	n/a
17	chr3:160121821-160121871	IMR90	lung:	fetal
18	chr3:160121821-160121871	BJ	skin:	n/a
19	chr3:160121821-160121871	SKMC	muscle:	n/a
20	chr3:160121821-160121871	ECC-1	luminal epithelium:	n/a
21	chr3:160121821-160121871	AG10803	skin:	n/a
22	chr3:160121821-160121871	HCT-116	colon:	n/a
23	chr3:160121821-160121871	Jurkat	blood:	n/a
24	chr3:160121821-160121871	LNCaP	prostate:	n/a
25	chr3:160121821-160121871	SK-N-SH	brain:	n/a
26	chr3:160121821-160121871	HCM	heart:	n/a
27	chr3:160121821-160121871	HAEpiC	amniotic membrane:	n/a
28	chr3:160121821-160121871	SK-N-SH_RA	brain:	n/a
29	chr3:160121821-160121871	PANC-1	pancreas:	n/a
30	chr3:160121821-160121871	Hela-S3	cervix:	n/a
31	chr3:160121821-160121871	A549	lung:	n/a
32	chr3:160121821-160121871	NB4	blood:	n/a
33	chr3:160121821-160121871	GM06990	blood:	n/a
34	chr3:160121821-160121871	RPTEC	kidney:	n/a
35	chr3:160121821-160121871	BE2_C	brain:	n/a
36	chr3:160121821-160121871	PFSK-1	brain:	n/a
37	chr3:160121821-160121871	NHBE	bronchial:	n/a
38	chr3:160121821-160121871	H1-hESC	embryonic stem cell:	embryo
39	chr3:160121821-160121871	HRE	kidney:	n/a
40	chr3:160121821-160121871	AG04449	skin:	fetal
41	chr3:160121821-160121871	HIPEpiC	eye:	n/a
42	chr3:160121821-160121871	HCPEpiC	choroid plexus:	n/a
43	chr3:160121821-160121871	HPAEpiC	pulmonary alveolar:	n/a
44	chr3:160121821-160121871	U87	brain:	n/a
45	chr3:160121821-160121871	GM19239	blood:	n/a
46	chr3:160121821-160121871	GM12878	blood:	n/a
47	chr3:160121821-160121871	GM12892	blood:	n/a
48	chr3:160121821-160121871	NHDF-neo	bronchial:	n/a
49	chr3:160121821-160121871	SAEC	small airway:	n/a
50	chr3:160121821-160121871	AG09319	gingival:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160121669..160124122-chr3:160164375..160167615,4	MCF-7	breast:
2	chr3:160116116..160127665-chr3:160158037..160169627,42	K562	blood:
3	chr3:160116116..160124648-chr3:160162504..160168767,20	K562	blood:

No data

Variant related genes	Relation type
MIR16-2	TF binding region
IFT80	TF binding region
MIR15B	TF binding region
SMC4	TF binding region
MIR16-2	CpG island
MIR15B	CpG island
SMC4	CpG island
IFT80	CpG island
ENSG00000213186	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1047210	0.82[JPT][hapmap]
rs10923	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936203	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11706810	0.82[JPT][hapmap]
rs11708118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11709232	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11709336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11716413	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11719750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11720689	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12152435	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12630564	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12630770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12630956	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12632030	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12638633	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12639488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs16831207	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236494	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826137	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17826173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17826221	0.82[JPT][hapmap]
rs17826257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1873076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2095529	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2099496	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2275151	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3732706	0.88[ASW][hapmap];0.84[YRI][hapmap]
rs3773369	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679886	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4679892	0.83[EUR][1000 genomes]
rs4680581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680586	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56952700	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60395700	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441311	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6798183	0.82[JPT][hapmap]
rs6809153	0.82[JPT][hapmap]
rs73875254	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73875259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73875285	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73875290	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7620828	0.82[JPT][hapmap]
rs7627555	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10936201	IFT80,TRIM59	cis	brain	BrainEAC
rs10936201	IFT80	cis	parietal	SCAN
rs10936201	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs10936201	IFT80	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160116000-160122600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:160116200-160122000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:160116200-160122400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:160116200-160122400	Active TSS	Right Atrium	heart
5	chr3:160116200-160122600	Active TSS	NHDF-Ad	bronchial
6	chr3:160116200-160123000	Active TSS	Aorta	Aorta
7	chr3:160116400-160122400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:160116400-160122400	Active TSS	Thymus	Thymus
9	chr3:160116400-160122600	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:160116400-160123000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:160116600-160122000	Active TSS	Fetal Muscle Leg	muscle
12	chr3:160118000-160123400	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr3:160118800-160122400	Transcr. at gene 5' and 3'	K562	blood
14	chr3:160119000-160144600	Weak transcription	Spleen	Spleen
15	chr3:160119000-160145200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:160119200-160122200	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr3:160119200-160122400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:160119200-160122600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:160119400-160128000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:160119400-160129000	Weak transcription	Brain Angular Gyrus	brain
21	chr3:160119400-160130400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:160119400-160130400	Weak transcription	Left Ventricle	heart
23	chr3:160119400-160137800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:160119400-160144400	Weak transcription	Pancreas	Pancrea
25	chr3:160119400-160144600	Weak transcription	Gastric	stomach
26	chr3:160119600-160133800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:160119800-160122000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr3:160119800-160122600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:160119800-160126000	Weak transcription	Stomach Mucosa	stomach
30	chr3:160119800-160130000	Weak transcription	Placenta	Placenta
31	chr3:160119800-160130400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr3:160119800-160130400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:160119800-160130400	Weak transcription	Small Intestine	intestine
34	chr3:160119800-160130600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:160119800-160132400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:160119800-160132400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:160119800-160142000	Weak transcription	Psoas Muscle	Psoas
38	chr3:160119800-160144400	Weak transcription	Esophagus	oesophagus
39	chr3:160119800-160144600	Weak transcription	Lung	lung
40	chr3:160119800-160144600	Weak transcription	Ovary	ovary
41	chr3:160119800-160144600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:160119800-160145200	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:160119800-160146600	Weak transcription	HSMMtube	muscle
44	chr3:160119800-160151800	Weak transcription	Brain Substantia Nigra	brain
45	chr3:160120000-160122000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
46	chr3:160120000-160122400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:160120000-160123800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr3:160120000-160132400	Weak transcription	Right Ventricle	heart
49	chr3:160120200-160132200	Weak transcription	Adipose Nuclei	Adipose
50	chr3:160120200-160152400	Weak transcription	Brain Inferior Temporal Lobe	brain

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