Variant report

Variant	rs11714208
Chromosome Location	chr3:141295050-141295051
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	CTCF	chr3:141295020-141295170	HMEC	breast:	n/a	chr3:141295110-141295118
2	CTCF	chr3:141295040-141295190	AoAF	blood vessel:	n/a	chr3:141295110-141295118
3	RAD21	chr3:141294988-141295865	SK-N-SH	brain:	n/a	chr3:141295503-141295522 chr3:141295504-141295513
4	CTCF	chr3:141294913-141295848	A549	lung:	n/a	chr3:141295504-141295525 chr3:141295506-141295513 chr3:141295110-141295118 chr3:141295502-141295520
5	CTCF	chr3:141294980-141295130	AG04450	lung:	n/a	chr3:141295110-141295118
6	CTCF	chr3:141295019-141295881	SK-N-SH	brain:	n/a	chr3:141295504-141295525 chr3:141295506-141295513 chr3:141295110-141295118 chr3:141295502-141295520

No.	Distal block	Cell Line	Cell type
1	chr3:141000930..141002501-chr3:141293837..141295898,2	K562	blood:
2	chr3:141294935..141295765-chr3:141363408..141364356,4	MCF-7	breast:
3	chr3:141289820..141291967-chr3:141293825..141295688,2	MCF-7	breast:
4	chr3:141289287..141291021-chr3:141292681..141295308,2	MCF-7	breast:
5	chr3:141292412..141295097-chr3:141295843..141298423,3	K562	blood:

Variant related genes	Relation type
RASA2	TF binding region
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1077181	0.81[CEU][hapmap];0.93[MEX][hapmap]
rs11557453	1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11707656	0.81[EUR][1000 genomes]
rs11709875	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs11711318	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11713714	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11717144	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717842	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs12695740	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695741	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695743	0.93[ASW][hapmap];0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059128	0.93[MEX][hapmap]
rs13062809	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13067519	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072100	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs13078872	0.88[CEU][hapmap]
rs13083593	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs13084444	0.88[CEU][hapmap];0.85[MEX][hapmap]
rs13088429	0.84[CEU][hapmap]
rs13095168	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13099945	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1863870	0.85[CEU][hapmap];0.85[MEX][hapmap]
rs2312194	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs34317570	0.84[AMR][1000 genomes]
rs34342794	0.93[ASN][1000 genomes]
rs3732872	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3806647	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4334619	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769161	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs720663	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624941	1.00[JPT][hapmap]
rs7636914	0.85[MEX][hapmap]
rs7649666	1.00[JPT][hapmap]
rs7651511	0.84[AMR][1000 genomes]
rs9289629	0.88[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs9289634	0.92[CEU][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9808953	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9822575	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9823528	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9829588	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830055	0.92[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9833121	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836050	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9836818	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9837202	0.85[CEU][hapmap]
rs9838230	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838419	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9840159	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840697	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9843866	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9849180	0.88[CEU][hapmap];0.93[MEX][hapmap]
rs9850416	0.92[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs9865971	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9868956	0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9870749	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873042	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006237	chr3:141227525-141300722	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv1795799	chr3:141284383-141301451	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv1794809	chr3:141290177-141304631	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11714208	RASA2	cis	cerebellum	SCAN
rs11714208	ATP1B3	cis	cerebellum	SCAN
rs11714208	ACPL2	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141236400-141301000	Weak transcription	Brain Substantia Nigra	brain
2	chr3:141236400-141306600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:141236600-141297000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:141236600-141299400	Weak transcription	Gastric	stomach
5	chr3:141237000-141299400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:141243400-141299400	Weak transcription	Spleen	Spleen
7	chr3:141254800-141295200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:141254800-141299200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:141254800-141299400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:141254800-141299400	Weak transcription	Right Ventricle	heart
11	chr3:141254800-141319200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:141255200-141304800	Weak transcription	Ovary	ovary
13	chr3:141255200-141320000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:141255400-141319200	Weak transcription	Aorta	Aorta
15	chr3:141257000-141300200	Weak transcription	Pancreas	Pancrea
16	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
17	chr3:141268400-141297800	Weak transcription	Fetal Heart	heart
18	chr3:141271200-141299400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:141272600-141319200	Strong transcription	Dnd41	blood
20	chr3:141275800-141320600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:141276000-141299400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:141276200-141297000	Weak transcription	Lung	lung
23	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
24	chr3:141277200-141297000	Weak transcription	Thymus	Thymus
25	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:141277600-141296400	Weak transcription	Hela-S3	cervix
27	chr3:141277800-141312000	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:141278000-141296800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:141281800-141297000	Weak transcription	Fetal Intestine Small	intestine
30	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
31	chr3:141284600-141299200	Weak transcription	Fetal Stomach	stomach
32	chr3:141288000-141312400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:141288200-141295200	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:141288200-141320000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:141288400-141295200	Strong transcription	Primary B cells from cord blood	blood
36	chr3:141288400-141316400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr3:141288600-141295400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:141288600-141302800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:141288600-141308400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:141288600-141316400	Strong transcription	Primary B cells from peripheral blood	blood
41	chr3:141288800-141299800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:141289000-141311800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr3:141289000-141316600	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:141289200-141309000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:141289200-141316400	Strong transcription	Fetal Thymus	thymus
46	chr3:141289400-141301600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:141290200-141301600	Strong transcription	NH-A	brain
48	chr3:141290400-141299400	Weak transcription	Brain Anterior Caudate	brain
49	chr3:141290600-141297200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:141291000-141301200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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