Variant report

Variant	rs3775500
Chromosome Location	chr4:100743513-100743514
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:100740809..100746722-chr4:100867916..100872607,6	K562	blood:
2	chr4:100741071..100743736-chr4:100867756..100869487,2	MCF-7	breast:
3	chr4:100735043..100738034-chr4:100738478..100743711,4	K562	blood:
4	chr4:100743200..100746311-chr4:100755153..100758233,3	K562	blood:
5	chr4:100742423..100744425-chr4:100753530..100755293,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164031	Chromatin interaction
ENSG00000164032	Chromatin interaction
ENSG00000070190	Chromatin interaction
ENSG00000245322	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1044044	0.84[CEU][hapmap]
rs10516458	0.85[CEU][hapmap]
rs11097676	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11097677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11097678	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097680	0.89[ASW][hapmap]
rs11097681	0.85[CEU][hapmap]
rs11723286	0.89[ASW][hapmap]
rs11732776	0.95[JPT][hapmap]
rs11736218	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs11931053	0.88[ASW][hapmap]
rs11932783	0.85[CEU][hapmap]
rs11935458	0.90[CEU][hapmap]
rs11935615	0.90[CEU][hapmap]
rs11937985	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs11941799	0.94[ASW][hapmap];0.90[CEU][hapmap];0.86[GIH][hapmap];0.81[TSI][hapmap]
rs11944405	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs11944656	0.90[CEU][hapmap]
rs11945303	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs11947295	0.85[CEU][hapmap]
rs1365491	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1365492	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs1365495	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.96[ASN][1000 genomes]
rs1426735	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1465519	0.94[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17029552	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17029563	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17029573	0.89[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs17029583	0.84[ASN][1000 genomes]
rs17029673	0.83[ASW][hapmap];0.85[CEU][hapmap]
rs1863608	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1896166	0.95[JPT][hapmap]
rs1961323	0.95[JPT][hapmap]
rs1972698	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2017707	0.84[CEU][hapmap]
rs2081626	0.85[CEU][hapmap]
rs2114442	0.95[JPT][hapmap]
rs2276939	0.85[CEU][hapmap]
rs2282588	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs2298735	0.95[JPT][hapmap]
rs2866174	0.91[JPT][hapmap]
rs28679452	0.81[ASN][1000 genomes]
rs3733463	0.89[ASW][hapmap];0.95[CEU][hapmap];0.89[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs3737484	0.89[ASW][hapmap];0.85[CEU][hapmap];0.81[TSI][hapmap]
rs3756087	0.95[JPT][hapmap]
rs3775499	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3775501	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699764	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs4699765	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs55973331	0.85[EUR][1000 genomes]
rs56174126	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57798058	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs58391911	0.84[EUR][1000 genomes]
rs58534089	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6532833	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6532834	0.89[ASW][hapmap];0.81[CEU][hapmap];0.81[TSI][hapmap]
rs6532835	0.95[JPT][hapmap]
rs6813099	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6814181	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6814895	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6816635	0.83[ASW][hapmap]
rs6817649	0.85[CEU][hapmap];0.90[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs6829912	0.89[ASW][hapmap];0.85[CEU][hapmap];0.84[TSI][hapmap]
rs6832726	0.85[CEU][hapmap]
rs6848337	0.95[JPT][hapmap]
rs6848666	0.90[CEU][hapmap];0.83[GIH][hapmap];0.81[TSI][hapmap]
rs6849599	0.82[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6852487	0.81[CEU][hapmap]
rs6854536	0.95[JPT][hapmap]
rs715239	0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.97[ASN][1000 genomes]
rs7666640	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7676564	0.95[JPT][hapmap]
rs7684872	0.95[JPT][hapmap]
rs7686428	0.95[JPT][hapmap]
rs7686565	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7687842	1.00[ASN][1000 genomes]
rs7688733	0.99[ASN][1000 genomes]
rs7688737	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7689566	0.95[JPT][hapmap]
rs7692416	0.95[JPT][hapmap]
rs7697357	0.84[EUR][1000 genomes]
rs7698065	0.99[ASN][1000 genomes]
rs919132	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs919133	0.82[CHD][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3775500	MAPKSP1	cis	parietal	SCAN
rs3775500	MAPKSP1	cis	cerebellum	SCAN
rs3775500	RAP1GDS1	cis	parietal	SCAN
rs3775500	DNAJB14	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100738800-100744400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr4:100739200-100744000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:100739400-100743800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr4:100739600-100743800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr4:100739600-100745400	Weak transcription	Esophagus	oesophagus
6	chr4:100739800-100744400	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr4:100740000-100744200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:100740000-100745000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr4:100740000-100756600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr4:100740200-100744200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr4:100740200-100745000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr4:100740800-100744200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:100741000-100745200	Weak transcription	Colon Smooth Muscle	Colon
14	chr4:100741200-100744800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:100741400-100744800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:100741400-100756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr4:100741400-100758200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr4:100742000-100744200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr4:100742000-100744200	Flanking Active TSS	GM12878-XiMat	blood
20	chr4:100742200-100743800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:100742200-100744000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr4:100742200-100744200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr4:100742200-100744200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr4:100742200-100745200	Enhancers	Primary B cells from peripheral blood	blood
25	chr4:100742600-100743600	Enhancers	Primary T cells from cord blood	blood
26	chr4:100742600-100743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:100742600-100743800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr4:100742800-100744000	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr4:100742800-100744800	Weak transcription	NHEK	skin
30	chr4:100742800-100746200	Weak transcription	HMEC	breast
31	chr4:100742800-100756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr4:100743000-100743600	Enhancers	Fetal Heart	heart
33	chr4:100743000-100749400	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:100743200-100744000	Enhancers	Right Atrium	heart
35	chr4:100743200-100744000	ZNF genes & repeats	K562	blood
36	chr4:100743200-100744400	Enhancers	Primary hematopoietic stem cells	blood
37	chr4:100743400-100743600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr4:100743400-100743800	Enhancers	Spleen	Spleen
39	chr4:100743400-100744200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:100743400-100744200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr4:100743400-100744200	Enhancers	Left Ventricle	heart

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