Variant report

Variant	rs6198
Chromosome Location	chr5:142657621-142657622
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:142655877..142658006-chr5:142659926..142661730,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10042042	0.85[YRI][hapmap]
rs10052957	0.85[GIH][hapmap]
rs10076665	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10482633	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10482642	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10482650	0.81[AFR][1000 genomes]
rs10482689	0.81[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10482700	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10515521	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740747	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11740792	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1438731	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17287758	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17339831	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1837262	0.84[GIH][hapmap]
rs1866388	0.85[GIH][hapmap]
rs258750	0.85[GIH][hapmap]
rs2918416	0.85[GIH][hapmap]
rs2918417	0.85[GIH][hapmap]
rs2963149	0.85[GIH][hapmap]
rs4128428	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6188	0.85[GIH][hapmap]
rs72801052	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72801070	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72801079	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801081	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801083	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72801086	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72801088	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs852977	0.82[GIH][hapmap]
rs852982	0.82[GIH][hapmap]
rs860457	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825941	chr5:142568715-142728031	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	esv33748	chr5:142638267-142699595	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv5041	chr5:142653189-142697896	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6198	TAF7	cis	cerebellum	SCAN
rs6198	NR3C1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:142642600-142658200	Weak transcription	Osteobl	bone
2	chr5:142643000-142658000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr5:142646600-142672400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:142647800-142658800	Weak transcription	Hela-S3	cervix
5	chr5:142649000-142658000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:142650000-142674000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:142650200-142658000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:142650400-142658000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:142650600-142677200	Weak transcription	Aorta	Aorta
10	chr5:142650800-142659200	Weak transcription	Thymus	Thymus
11	chr5:142652200-142669800	Weak transcription	Left Ventricle	heart
12	chr5:142652400-142659400	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:142652800-142660200	Weak transcription	NH-A	brain
14	chr5:142653000-142658400	Weak transcription	Fetal Lung	lung
15	chr5:142653000-142671200	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:142653200-142658000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:142653200-142674800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:142654000-142659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr5:142654200-142659200	Weak transcription	HSMMtube	muscle
20	chr5:142654600-142659400	Strong transcription	GM12878-XiMat	blood
21	chr5:142654600-142666600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr5:142654800-142658200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:142654800-142658400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:142654800-142659400	Weak transcription	NHLF	lung
25	chr5:142654800-142663600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:142655000-142664800	Weak transcription	NHEK	skin
27	chr5:142655000-142669800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr5:142655000-142671600	Weak transcription	K562	blood
29	chr5:142655200-142662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:142655200-142674000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr5:142655200-142674200	Weak transcription	Brain Angular Gyrus	brain
32	chr5:142655400-142661400	Weak transcription	Placenta	Placenta
33	chr5:142655400-142672600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:142655600-142658200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr5:142655600-142658800	Weak transcription	Fetal Muscle Trunk	muscle
36	chr5:142655800-142658000	Weak transcription	Fetal Thymus	thymus
37	chr5:142655800-142658600	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr5:142655800-142660600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:142655800-142662000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr5:142655800-142664600	Strong transcription	NHDF-Ad	bronchial
41	chr5:142655800-142669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:142655800-142670200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr5:142655800-142671800	Weak transcription	Psoas Muscle	Psoas
44	chr5:142655800-142677200	Weak transcription	Spleen	Spleen
45	chr5:142655800-142699200	Strong transcription	Dnd41	blood
46	chr5:142656000-142658000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr5:142656000-142658000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:142656000-142658200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:142656000-142658400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr5:142656000-142659800	Enhancers	Liver	Liver

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