Variant report

Variant	rs259938
Chromosome Location	chr6:30008003-30008004
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30006360..30008334-chr6:30017621..30020296,2	MCF-7	breast:
2	chr6:30006290..30008332-chr6:30012073..30013953,2	K562	blood:
3	chr6:30006757..30011718-chr6:30026888..30030646,5	K562	blood:

Variant related genes	Relation type
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1150736	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150741	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1150742	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1150743	0.91[ASN][1000 genomes]
rs1245371	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1245503	0.89[ASN][1000 genomes]
rs2246555	0.93[ASN][1000 genomes]
rs2530388	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259919	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs259921	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259923	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259929	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259931	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs259933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs259940	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs259943	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2735064	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2735066	0.93[ASN][1000 genomes]
rs2735067	0.94[ASN][1000 genomes]
rs356954	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356961	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356966	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356967	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356968	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356969	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401618	0.94[ASN][1000 genomes]
rs9260910	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv884045	chr6:29997312-30015905	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv884046	chr6:29997312-30023868	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1842358	chr6:30003764-30008996	Weak transcription Strong transcription Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv819291	chr6:30003841-30009815	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv884048	chr6:30005754-30021740	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs259938	Hs.519979	cis	multi-tissue	Pritchard
rs259938	ZNRD1	Cis_1M	lymphoblastoid	RTeQTL
rs259938	C6orf12	Cis_1M	lymphoblastoid	RTeQTL
rs259938	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs259938	LOC347981	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29976600-30023000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:29977200-30024600	Weak transcription	Brain Anterior Caudate	brain
6	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
8	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:29979400-30024600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:29979600-30022800	Weak transcription	Ovary	ovary
11	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
12	chr6:29980200-30012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:29981200-30023000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:29981800-30010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:29982800-30009800	Weak transcription	Psoas Muscle	Psoas
16	chr6:29982800-30022800	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:29983400-30012400	Weak transcription	NHEK	skin
18	chr6:29984600-30023400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:29985000-30024600	Weak transcription	Brain Angular Gyrus	brain
20	chr6:29985400-30008200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr6:29987800-30010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
23	chr6:29988000-30010400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:29988200-30009800	Weak transcription	HepG2	liver
25	chr6:29988200-30022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
28	chr6:29988400-30021600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
30	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
31	chr6:29988600-30009800	Weak transcription	Left Ventricle	heart
32	chr6:29988600-30022200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr6:29988800-30022800	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:29989000-30009800	Weak transcription	GM12878-XiMat	blood
36	chr6:29989000-30023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:29989400-30021400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:29996600-30012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:29998400-30012200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:29998400-30012200	Weak transcription	HMEC	breast
42	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
43	chr6:29999800-30012400	Weak transcription	Hela-S3	cervix
44	chr6:29999800-30022200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr6:30001200-30025000	Weak transcription	Fetal Lung	lung
47	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
48	chr6:30001400-30012000	Weak transcription	HSMM	muscle
49	chr6:30001600-30022600	Weak transcription	Brain Substantia Nigra	brain
50	chr6:30001800-30012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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