Variant report

Variant	rs295323
Chromosome Location	chr3:141327474-141327475
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141326204..141327732-chr3:141330355..141332804,2	K562	blood:
2	chr3:141325633..141327918-chr3:141334802..141336687,2	MCF-7	breast:
3	chr3:141326316..141328751-chr3:141631942..141633782,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11711375	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11916906	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11917587	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13062809	0.87[EUR][1000 genomes]
rs13069717	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1366042	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap]
rs1493209	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1582875	0.92[CEU][hapmap];0.91[YRI][hapmap]
rs16851435	0.87[CHD][hapmap];0.89[JPT][hapmap]
rs16851438	0.94[JPT][hapmap]
rs16851441	0.88[JPT][hapmap]
rs16851483	0.88[JPT][hapmap]
rs1863867	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs2035935	0.88[JPT][hapmap]
rs2035936	0.82[JPT][hapmap]
rs2042864	0.92[CEU][hapmap];0.91[YRI][hapmap]
rs2172471	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2312193	0.89[CEU][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap]
rs2639997	0.88[JPT][hapmap]
rs2639998	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2640017	0.88[JPT][hapmap]
rs295299	0.88[JPT][hapmap]
rs295300	0.81[CHB][hapmap];0.92[CHD][hapmap];0.88[JPT][hapmap]
rs295320	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35711802	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732869	0.88[JPT][hapmap]
rs3806646	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs3821709	0.88[JPT][hapmap]
rs3821710	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821712	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683610	0.88[JPT][hapmap]
rs6440013	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440015	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6763498	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767158	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6776003	0.85[CEU][hapmap];0.88[ASN][1000 genomes]
rs6785874	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800122	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6808837	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627807	0.88[JPT][hapmap]
rs7632308	0.92[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap]
rs7643837	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813177	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[GIH][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9851256	0.82[CEU][hapmap]
rs9878347	0.94[JPT][hapmap];0.82[YRI][hapmap]
rs9879503	0.94[JPT][hapmap];0.82[YRI][hapmap]

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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs295323	RASA2	cis	parietal	SCAN
rs295323	ZBTB38	cis	cerebellum	SCAN
rs295323	GK5	cis	parietal	SCAN
rs295323	ATP1B3	cis	cerebellum	SCAN
rs295323	RASA2	cis	cerebellum	SCAN
rs295323	RASA2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141276400-141329400	Weak transcription	Small Intestine	intestine
3	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:141281800-141329400	Weak transcription	Fetal Brain Male	brain
5	chr3:141298000-141328400	Weak transcription	Hela-S3	cervix
6	chr3:141300200-141328800	Weak transcription	K562	blood
7	chr3:141305200-141329000	Weak transcription	NHLF	lung
8	chr3:141306200-141328800	Weak transcription	Right Ventricle	heart
9	chr3:141307400-141328400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:141313400-141328800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:141315000-141328800	Weak transcription	Colonic Mucosa	Colon
13	chr3:141315200-141328800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:141315800-141328600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:141319400-141329400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:141319600-141329000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:141319600-141329600	Weak transcription	HSMMtube	muscle
18	chr3:141320200-141328800	Weak transcription	Spleen	Spleen
19	chr3:141320200-141329000	Weak transcription	Pancreas	Pancrea
20	chr3:141320200-141329400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:141320400-141331000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:141320400-141333600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:141320400-141337200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:141321400-141328800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:141321400-141328800	Weak transcription	Ovary	ovary
26	chr3:141321400-141329000	Weak transcription	Esophagus	oesophagus
27	chr3:141321400-141329800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:141321600-141327600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:141321600-141331800	Weak transcription	Brain Substantia Nigra	brain
30	chr3:141321800-141328800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:141321800-141328800	Weak transcription	Fetal Intestine Small	intestine
32	chr3:141321800-141329000	Weak transcription	Fetal Stomach	stomach
33	chr3:141321800-141329600	Weak transcription	A549	lung
34	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:141322200-141329000	Weak transcription	Fetal Muscle Leg	muscle
36	chr3:141324000-141333800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr3:141324200-141333600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:141324200-141336000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr3:141324600-141329400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:141324600-141332000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:141324800-141330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:141324800-141332200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:141324800-141334000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:141325000-141328600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:141325000-141328800	Weak transcription	Left Ventricle	heart
46	chr3:141325000-141329400	Weak transcription	Aorta	Aorta
47	chr3:141325000-141329400	Weak transcription	Gastric	stomach
48	chr3:141325000-141330000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:141325000-141332200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:141325000-141338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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