Variant report

Variant	rs7371987
Chromosome Location	chr3:46318508-46318509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:46317738..46318586-chr3:46409721..46410429,5	MCF-7	breast:
2	chr3:46317898..46318782-chr3:46409428..46410356,4	MCF-7	breast:
3	chr3:46317124..46320589-chr3:46407994..46411912,3	MCF-7	breast:
4	chr3:46317715..46318633-chr3:46413664..46414217,2	K562	blood:
5	chr3:46318130..46320432-chr3:46322132..46324607,2	K562	blood:

Variant related genes	Relation type
ENSG00000160791	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs13081325	0.89[EUR][1000 genomes]
rs13084656	0.90[JPT][hapmap]
rs13096142	0.90[JPT][hapmap];0.86[MEX][hapmap]
rs1388604	0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1979672	0.88[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs2040389	0.84[EUR][1000 genomes]
rs2040390	0.83[EUR][1000 genomes]
rs2097283	0.83[EUR][1000 genomes]
rs2157058	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187669	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2187670	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2213288	0.83[EUR][1000 genomes]
rs3092962	0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3092964	0.80[EUR][1000 genomes]
rs34708505	0.81[EUR][1000 genomes]
rs34997146	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35510257	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36048784	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36118141	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3762823	0.81[MEX][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs3918359	0.80[EUR][1000 genomes]
rs3918361	0.80[EUR][1000 genomes]
rs41276529	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41418050	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs41502550	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682812	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683194	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683198	0.81[ASN][1000 genomes]
rs4683199	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4683211	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683215	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4683218	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62244813	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441953	0.81[ASN][1000 genomes]
rs6441958	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441959	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6441960	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441963	0.90[JPT][hapmap]
rs6441968	0.82[EUR][1000 genomes]
rs6441971	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs67450950	0.80[EUR][1000 genomes]
rs6765031	0.80[EUR][1000 genomes]
rs6783993	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788849	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801761	0.82[EUR][1000 genomes]
rs6810232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71327045	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71615444	0.83[ASN][1000 genomes]
rs7432080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs743660	0.81[MEX][hapmap];0.84[TSI][hapmap]
rs7612940	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7635588	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7650093	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs768539	0.80[EUR][1000 genomes]
rs9839623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9840204	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9842716	0.90[JPT][hapmap]
rs9853223	0.90[JPT][hapmap]
rs9877860	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7371987	ABHD5	cis	parietal	SCAN
rs7371987	RBM5	cis	parietal	SCAN
rs7371987	CXCR6	cis	parietal	SCAN
rs7371987	KLHL18	cis	parietal	SCAN
rs7371987	SS18L2	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46317600-46324600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:46317600-46329200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:46317800-46319400	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr3:46317800-46329200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:46318000-46318600	Enhancers	Primary B cells from peripheral blood	blood
6	chr3:46318000-46319000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:46318000-46319000	Enhancers	Placenta	Placenta
8	chr3:46318000-46319200	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr3:46318000-46319400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:46318000-46319400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:46318000-46319400	Enhancers	Fetal Thymus	thymus
12	chr3:46318000-46319600	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr3:46318000-46319800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:46318000-46331400	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:46318200-46318600	Enhancers	Primary B cells from cord blood	blood
16	chr3:46318200-46318800	Enhancers	Spleen	Spleen
17	chr3:46318200-46319400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr3:46318200-46319400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr3:46318200-46319400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:46318200-46319400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr3:46318200-46319400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:46318400-46319000	Enhancers	Primary T cells from cord blood	blood
23	chr3:46318400-46319200	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:46318400-46319200	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr3:46318400-46319400	Enhancers	Rectal Mucosa Donor 31	rectum

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