Variant report

Variant	rs4149509
Chromosome Location	chr2:101023699-101023700
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:101022665..101026054-chr2:101026732..101029227,3	K562	blood:
2	chr2:101018004..101019517-chr2:101023470..101025341,2	K562	blood:
3	chr2:101016960..101020223-chr2:101021855..101026333,5	K562	blood:
4	chr2:101023081..101025478-chr2:101042210..101044979,2	MCF-7	breast:
5	chr2:101018059..101019912-chr2:101021357..101024313,2	MCF-7	breast:
6	chr2:101022190..101024904-chr2:101032493..101034257,2	K562	blood:

Variant related genes	Relation type
ENSG00000115526	Chromatin interaction

Extended variants
information (count: 127 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10167159	0.84[AMR][1000 genomes]
rs10172841	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10176978	0.83[ASN][1000 genomes]
rs10180570	0.93[AMR][1000 genomes]
rs10180685	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10183063	0.95[ASN][1000 genomes]
rs10184899	0.81[AMR][1000 genomes]
rs10193535	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes]
rs10206374	0.96[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1057056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1057063	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1057064	1.00[CHB][hapmap]
rs1124009	1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13391930	0.81[AMR][1000 genomes]
rs13396147	0.81[AMR][1000 genomes]
rs13400841	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13404823	0.81[AMR][1000 genomes]
rs13407408	0.81[AMR][1000 genomes]
rs13407648	0.81[AMR][1000 genomes]
rs13407891	0.81[AMR][1000 genomes]
rs13410582	0.81[AMR][1000 genomes]
rs13419808	0.81[AMR][1000 genomes]
rs1347721	0.87[AMR][1000 genomes]
rs1370627	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs1437972	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.93[ASN][1000 genomes]
rs1465829	0.85[CHD][hapmap]
rs17024034	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs17024035	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs17024129	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs17024133	0.90[GIH][hapmap]
rs17024136	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs17024144	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs17024203	0.85[CHD][hapmap]
rs17024207	0.85[CHD][hapmap]
rs17024209	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1898571	0.81[AMR][1000 genomes]
rs1898573	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2083148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2309801	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3748934	0.85[CHD][hapmap]
rs3748936	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3791358	1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs4149506	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4149514	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4149515	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4149516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4149522	0.85[CHD][hapmap]
rs4850932	0.88[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55640826	0.81[AMR][1000 genomes]
rs55843950	0.81[AMR][1000 genomes]
rs55932868	0.93[ASN][1000 genomes]
rs56118658	0.81[AMR][1000 genomes]
rs56656536	0.90[AMR][1000 genomes]
rs56741959	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57862179	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58164864	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58674788	0.93[ASN][1000 genomes]
rs59701896	0.93[ASN][1000 genomes]
rs59858985	0.93[ASN][1000 genomes]
rs60468180	1.00[ASN][1000 genomes]
rs60566188	0.93[ASN][1000 genomes]
rs60609848	0.90[AMR][1000 genomes]
rs60898093	0.81[AMR][1000 genomes]
rs61321970	0.80[AMR][1000 genomes]
rs61710328	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542933	0.93[ASN][1000 genomes]
rs6542945	0.93[ASN][1000 genomes]
rs6542946	0.94[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs6706707	0.93[ASN][1000 genomes]
rs6716009	0.81[AMR][1000 genomes]
rs6716367	0.90[AMR][1000 genomes]
rs6724695	0.81[AMR][1000 genomes]
rs6725672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728575	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs6732285	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs6736938	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6738566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6739589	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6749572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750040	1.00[CHB][hapmap]
rs6754869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6755285	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6758161	0.81[AMR][1000 genomes]
rs6758622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761084	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72960184	0.81[AMR][1000 genomes]
rs72960186	0.81[AMR][1000 genomes]
rs72960202	0.81[AMR][1000 genomes]
rs73966105	0.93[ASN][1000 genomes]
rs73966106	0.93[ASN][1000 genomes]
rs73968413	0.93[ASN][1000 genomes]
rs7559084	0.93[ASN][1000 genomes]
rs7559939	0.81[AMR][1000 genomes]
rs7559946	0.81[AMR][1000 genomes]
rs7561065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562184	0.93[ASN][1000 genomes]
rs7562461	0.81[AMR][1000 genomes]
rs7562479	0.81[AMR][1000 genomes]
rs7562486	0.81[AMR][1000 genomes]
rs7562615	0.81[AMR][1000 genomes]
rs7562636	0.93[ASN][1000 genomes]
rs7562754	0.93[ASN][1000 genomes]
rs7564178	0.84[AMR][1000 genomes]
rs7565502	0.93[ASN][1000 genomes]
rs7567130	1.00[CEU][hapmap];0.95[ASN][1000 genomes]
rs7571410	0.93[ASN][1000 genomes]
rs7571651	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7571659	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7572119	0.81[AMR][1000 genomes]
rs7574684	0.81[AMR][1000 genomes]
rs7575422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576749	0.81[AMR][1000 genomes]
rs7582096	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7582546	0.81[AMR][1000 genomes]
rs7585713	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7585898	1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs7587333	0.93[AMR][1000 genomes]
rs7596483	0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7598205	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs7598227	0.93[ASN][1000 genomes]
rs7605834	0.93[ASN][1000 genomes]
rs876439	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[ASN][1000 genomes]
rs9308834	0.90[AMR][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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv916792	chr2:101021066-101525200	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4149509	PTGS2	trans	brain	seeQTL
rs4149509	NPAS4	trans	brain	seeQTL
rs4149509	EGR1	trans	brain	seeQTL
rs4149509	SLC25A25	trans	brain	seeQTL
rs4149509	EGR4	trans	brain	seeQTL
rs4149509	ARC	trans	brain	seeQTL
rs4149509	FOSB	trans	brain	seeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:101005600-101032800	Weak transcription	HUVEC	blood vessel
2	chr2:101005800-101033000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr2:101006600-101031600	Strong transcription	Fetal Stomach	stomach
4	chr2:101007000-101025000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:101007000-101027200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr2:101007200-101032000	Weak transcription	NHDF-Ad	bronchial
7	chr2:101007600-101024200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:101007600-101030600	Weak transcription	NH-A	brain
9	chr2:101007800-101023800	Strong transcription	Fetal Muscle Trunk	muscle
10	chr2:101007800-101024000	Weak transcription	Liver	Liver
11	chr2:101008000-101033000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:101008400-101025200	Weak transcription	Fetal Brain Male	brain
13	chr2:101009400-101026400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:101010200-101032800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:101012000-101024000	Weak transcription	Fetal Heart	heart
16	chr2:101013200-101030400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:101013200-101033000	Weak transcription	Fetal Intestine Large	intestine
18	chr2:101014400-101033200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:101014800-101032400	Weak transcription	Hela-S3	cervix
20	chr2:101015600-101033000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr2:101015800-101024400	Strong transcription	Fetal Brain Female	brain
22	chr2:101015800-101024400	Strong transcription	Fetal Muscle Leg	muscle
23	chr2:101016000-101023800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:101016400-101028000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:101016400-101032600	Weak transcription	HSMM	muscle
26	chr2:101016800-101024800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:101017000-101032800	Weak transcription	Osteobl	bone
28	chr2:101017200-101024800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:101017400-101024000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:101017400-101024200	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr2:101017400-101026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:101017400-101026600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:101017600-101024000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:101017600-101024200	Strong transcription	Adipose Nuclei	Adipose
35	chr2:101017600-101024400	Strong transcription	Dnd41	blood
36	chr2:101017600-101027000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:101017800-101023800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:101017800-101023800	Strong transcription	GM12878-XiMat	blood
39	chr2:101018000-101024000	Strong transcription	HepG2	liver
40	chr2:101018400-101023800	Strong transcription	Right Ventricle	heart
41	chr2:101018400-101024200	Strong transcription	Gastric	stomach
42	chr2:101018400-101033000	Weak transcription	Primary B cells from cord blood	blood
43	chr2:101018600-101024000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr2:101019000-101032800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:101019600-101024200	Strong transcription	Primary T cells from cord blood	blood
46	chr2:101020200-101024200	Strong transcription	Aorta	Aorta
47	chr2:101020200-101024400	Strong transcription	Spleen	Spleen
48	chr2:101020400-101023800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:101020400-101024000	Strong transcription	Fetal Intestine Small	intestine
50	chr2:101020400-101024200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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