Variant report

Variant	rs6846414
Chromosome Location	chr4:10586530-10586531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:10584329..10586994-chr4:10592921..10595277,2	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11934521	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11938495	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17382947	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17382963	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17383005	1.00[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17383033	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17383040	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17383095	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383130	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17383186	0.85[CHB][hapmap]
rs17467476	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17467581	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17467602	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17467609	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1966375	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1989245	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1990272	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2014303	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2302170	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2869470	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2904113	0.83[YRI][hapmap]
rs35265323	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41340151	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55804861	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55878273	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56325310	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58442828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58728006	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59203169	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61495782	0.97[ASN][1000 genomes]
rs61795106	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61795107	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6448068	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6816045	1.00[CHB][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6818298	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6819450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MKK][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6837268	0.93[EUR][1000 genomes]
rs6848059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6855648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6856210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73228207	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73228210	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73228212	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73228224	0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs73228227	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73228228	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73228236	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7439618	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs763677	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7657440	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7659607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7674488	0.97[ASN][1000 genomes]
rs7683820	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7685040	0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7685227	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7694378	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7696635	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
5	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
6	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
7	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
8	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
9	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
10	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
11	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
12	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
13	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
15	nsv593727	chr4:10397327-10694991	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
18	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv878698	chr4:10536544-10632404	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6846414	GRPEL1	cis	cerebellum	SCAN
rs6846414	SORCS2	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10583600-10590800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr4:10584600-10588000	Enhancers	Fetal Thymus	thymus
3	chr4:10585000-10586600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:10585000-10586600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:10585200-10586600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr4:10585200-10586600	Enhancers	Placenta	Placenta
7	chr4:10585200-10586800	Enhancers	Thymus	Thymus
8	chr4:10585600-10586600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr4:10585600-10586600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr4:10585600-10586600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:10585600-10586600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:10585800-10586600	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr4:10585800-10586600	Enhancers	Primary hematopoietic stem cells	blood
14	chr4:10585800-10589000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:10585800-10591600	Weak transcription	HSMM	muscle
16	chr4:10586000-10586600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:10586000-10586600	Enhancers	NHEK	skin
18	chr4:10586000-10589400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr4:10586000-10591000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:10586000-10591400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:10586000-10591400	Weak transcription	Primary B cells from cord blood	blood
22	chr4:10586200-10586600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr4:10586200-10589200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:10586200-10589400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr4:10586200-10589400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:10586200-10591000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:10586200-10591000	Weak transcription	Spleen	Spleen
28	chr4:10586400-10586600	Enhancers	GM12878-XiMat	blood
29	chr4:10586400-10586600	Enhancers	NHLF	lung
30	chr4:10586400-10586800	Enhancers	Dnd41	blood
31	chr4:10586400-10587600	Weak transcription	Osteobl	bone
32	chr4:10586400-10588600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:10586400-10588800	Weak transcription	Primary T cells from cord blood	blood
34	chr4:10586400-10590800	Weak transcription	Fetal Muscle Leg	muscle
35	chr4:10586400-10591000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:10586400-10591000	Weak transcription	NH-A	brain
37	chr4:10586400-10591400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:10586400-10591400	Weak transcription	Muscle Satellite Cultured Cells	--

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