Variant report

Variant	rs3775499
Chromosome Location	chr4:100743145-100743146
allele	A/C/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	chr4:100742423..100744425-chr4:100753530..100755293,2	MCF-7	breast:

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

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11097676	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11097677	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11097678	1.00[ASN][1000 genomes]
rs11732776	0.95[JPT][hapmap]
rs1365491	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1365492	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs1365495	0.88[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.96[ASN][1000 genomes]
rs1426735	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17029552	1.00[ASN][1000 genomes]
rs17029563	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs17029583	0.84[ASN][1000 genomes]
rs1863608	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1896166	0.95[JPT][hapmap]
rs1961323	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs1972698	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2114442	0.95[JPT][hapmap]
rs2162386	0.96[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2282588	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298735	0.95[JPT][hapmap]
rs2866174	0.91[JPT][hapmap]
rs28679452	0.81[ASN][1000 genomes]
rs3756087	0.95[JPT][hapmap]
rs3775500	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3775501	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3822103	0.96[CEU][hapmap];0.92[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4699764	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699765	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs56174126	0.99[ASN][1000 genomes]
rs6532833	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532835	0.95[JPT][hapmap]
rs6814895	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848337	0.95[JPT][hapmap]
rs6849599	0.85[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6854536	0.95[JPT][hapmap]
rs715239	0.88[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.87[JPT][hapmap];0.97[ASN][1000 genomes]
rs7676564	0.95[JPT][hapmap]
rs7684872	0.95[JPT][hapmap]
rs7686428	0.95[JPT][hapmap]
rs7687842	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7688733	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7689566	0.95[JPT][hapmap]
rs7692416	0.95[JPT][hapmap]
rs7698065	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919132	0.81[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs919133	0.81[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3775499	DNAJB14	cis	parietal	SCAN
rs3775499	MAPKSP1	cis	parietal	SCAN
rs3775499	DAPP1	Cis_1M	lymphoblastoid	RTeQTL
rs3775499	KLHL12	trans	cerebellum	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	chr4:100740600-100743200	Weak transcription	K562	blood
13	chr4:100740800-100744200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr4:100741000-100743200	Active TSS	Right Atrium	heart
15	chr4:100741000-100745200	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:100741200-100743400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:100741200-100744800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr4:100741400-100743400	Weak transcription	Spleen	Spleen
19	chr4:100741400-100744800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr4:100741400-100756800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:100741400-100758200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:100742000-100743400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:100742000-100744200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr4:100742000-100744200	Flanking Active TSS	GM12878-XiMat	blood
25	chr4:100742200-100743800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr4:100742200-100744000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:100742200-100744200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr4:100742200-100744200	Enhancers	Placenta Amnion	Placenta Amnion
29	chr4:100742200-100745200	Enhancers	Primary B cells from peripheral blood	blood
30	chr4:100742400-100743200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr4:100742600-100743600	Enhancers	Primary T cells from cord blood	blood
32	chr4:100742600-100743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr4:100742600-100743800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:100742800-100743400	Weak transcription	Left Ventricle	heart
35	chr4:100742800-100744000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr4:100742800-100744800	Weak transcription	NHEK	skin
37	chr4:100742800-100746200	Weak transcription	HMEC	breast
38	chr4:100742800-100756400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:100743000-100743400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr4:100743000-100743600	Enhancers	Fetal Heart	heart
41	chr4:100743000-100749400	Enhancers	Primary monocytes fromperipheralblood	blood

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