Variant report

Variant	rs3737240
Chromosome Location	chr1:150483355-150483356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150336131..150338597-chr1:150480002..150483403,3	MCF-7	breast:
2	chr1:150458274..150463765-chr1:150483214..150490747,8	K562	blood:
3	chr1:150482969..150486051-chr1:150520372..150524446,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TARS2-1	chr1:150483352-150483622	NONHSAT006296

Variant related genes	Relation type
ENSG00000264553	Chromatin interaction
ENSG00000163125	Chromatin interaction
ENSG00000143382	Chromatin interaction
ENSG00000143374	Chromatin interaction
ENSG00000225996	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11205373	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs11205385	0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11577600	0.86[CEU][hapmap]
rs11577843	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs11581351	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs11582423	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11587116	0.80[ASN][1000 genomes]
rs11587575	0.87[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes]
rs11590324	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12023378	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12029359	0.87[CHB][hapmap]
rs12040949	0.80[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs12042229	0.84[AMR][1000 genomes]
rs12042579	0.85[AMR][1000 genomes]
rs12046446	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12046899	0.87[CHB][hapmap]
rs1260367	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1260389	0.81[AMR][1000 genomes]
rs1260407	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs1260411	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1260459	0.88[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap]
rs13294	0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1498308	0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs1625468	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs1694364	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs1694377	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs1694380	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs17596326	0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes]
rs17597088	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1815544	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1932934	0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs1972031	0.84[AMR][1000 genomes]
rs2794679	0.90[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap]
rs2794681	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2867893	0.80[ASN][1000 genomes]
rs2867894	0.80[ASN][1000 genomes]
rs2873669	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes]
rs3738487	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820544	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3896342	0.84[AMR][1000 genomes]
rs4446975	0.87[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs4451552	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs488271	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4926395	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs4926437	0.84[AMR][1000 genomes]
rs4971010	0.88[JPT][hapmap]
rs55823828	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55928222	0.84[AMR][1000 genomes]
rs55996928	0.81[AMR][1000 genomes]
rs578353	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs59898460	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6662108	0.88[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs6672808	0.84[AMR][1000 genomes]
rs6703652	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs696616	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs696618	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs698913	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs698916	0.88[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs698923	0.82[AMR][1000 genomes]
rs7002	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes]
rs7513205	0.92[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7517441	0.84[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap]
rs7523428	0.82[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs7539458	0.84[AMR][1000 genomes]
rs7548085	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7553867	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs832622	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs834229	0.82[AMR][1000 genomes]
rs834230	0.82[AMR][1000 genomes]
rs834231	0.88[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs834232	0.87[CEU][hapmap];0.93[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs834234	0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs834242	0.87[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs9436007	0.84[AMR][1000 genomes]
rs9436008	0.81[AMR][1000 genomes]
rs9436112	0.87[CEU][hapmap];0.94[JPT][hapmap]
rs9436115	0.81[AMR][1000 genomes]
rs9436125	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9436127	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][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	nsv916014	chr1:150187139-150537483	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
2	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers 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	175 gene(s)	inside rSNPs	diseases
3	esv1814231	chr1:150479528-150540117	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3737240	LCE2A	cis	parietal	SCAN
rs3737240	SNX27	cis	parietal	SCAN
rs3737240	CTSK	cis	cerebellum	SCAN
rs3737240	MRPS21	cis	cerebellum	SCAN
rs3737240	MRPS21	cis	parietal	SCAN
rs3737240	POLR3GL	cis	cerebellum	SCAN
rs3737240	CTSS	cis	cerebellum	SCAN
rs3737240	POGZ	cis	cerebellum	SCAN
rs3737240	TARS2	cis	cerebellum	SCAN
rs3737240	C1orf54	cis	parietal	SCAN
rs3737240	SEC22B	cis	parietal	SCAN
rs3737240	MRPS21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150461000-150486800	Weak transcription	Fetal Heart	heart
2	chr1:150462000-150485800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:150468800-150483800	Strong transcription	Brain Germinal Matrix	brain
4	chr1:150471800-150487400	Weak transcription	Fetal Brain Male	brain
5	chr1:150475000-150485400	Strong transcription	Fetal Brain Female	brain
6	chr1:150476200-150486200	Strong transcription	Ovary	ovary
7	chr1:150477800-150487400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:150478200-150487400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:150478800-150487200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:150478800-150487400	Weak transcription	Psoas Muscle	Psoas
11	chr1:150478800-150487600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:150479000-150484200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:150479000-150487400	Weak transcription	Fetal Lung	lung
14	chr1:150479000-150487600	Weak transcription	Aorta	Aorta
15	chr1:150479400-150483400	Weak transcription	Gastric	stomach
16	chr1:150479400-150487400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:150479400-150487600	Weak transcription	Fetal Kidney	kidney
18	chr1:150479600-150483800	Weak transcription	Pancreas	Pancrea
19	chr1:150479600-150487200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:150479600-150487200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:150479600-150487400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:150479600-150487400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:150479600-150487400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr1:150479600-150487400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:150479600-150487400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:150479600-150487400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:150479600-150487400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:150479600-150487600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:150479800-150485600	Weak transcription	Fetal Thymus	thymus
30	chr1:150479800-150487200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:150479800-150487400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:150479800-150487400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr1:150480000-150487200	Weak transcription	Primary B cells from cord blood	blood
34	chr1:150480000-150487200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:150480200-150487200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr1:150480400-150485400	Genic enhancers	Spleen	Spleen
37	chr1:150480400-150487400	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr1:150480600-150487200	Weak transcription	Fetal Intestine Large	intestine
39	chr1:150480600-150487400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:150480800-150483400	Weak transcription	Liver	Liver
41	chr1:150480800-150483400	Weak transcription	Brain Anterior Caudate	brain
42	chr1:150480800-150484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:150480800-150485000	Transcr. at gene 5' and 3'	Esophagus	oesophagus
44	chr1:150480800-150487400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:150480800-150487400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:150480800-150487400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:150480800-150487400	Weak transcription	Dnd41	blood
48	chr1:150481000-150483600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:150481000-150484200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:150481000-150484200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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