Variant report

Variant	rs9261212
Chromosome Location	chr6:30008996-30008997
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	chr6:30003872..30007108-chr6:30008649..30012245,4	K562	blood:
2	chr6:30006757..30011718-chr6:30026888..30030646,5	K562	blood:

Variant related genes	Relation type
ENSG00000204623	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1061536	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632873	0.84[ASN][1000 genomes]
rs3016019	0.84[ASN][1000 genomes]
rs3094145	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121596	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3121597	0.83[ASN][1000 genomes]
rs3132128	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132683	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893259	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3893465	0.83[EUR][1000 genomes]
rs4472395	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4959036	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5025708	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763159	0.94[EUR][1000 genomes]
rs9260676	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260685	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260702	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260706	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260761	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260786	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260808	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260857	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260973	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9260997	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261061	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261136	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261142	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9261143	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261211	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261269	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261402	0.88[AMR][1000 genomes];0.95[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9261212	ZKSCAN3	cis	cerebellum	SCAN
rs9261212	DSG2	trans	lymphoblastoid	seeQTL
rs9261212	GRM4	cis	cerebellum	SCAN
rs9261212	HIST1H2BF	cis	parietal	SCAN

Chromatin state (count:68 , 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	chr6:29987800-30010600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr6:29987800-30024800	Weak transcription	Fetal Intestine Large	intestine
22	chr6:29988000-30010400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr6:29988200-30009800	Weak transcription	HepG2	liver
24	chr6:29988200-30022800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
27	chr6:29988400-30021600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:29988400-30023400	Weak transcription	Adipose Nuclei	Adipose
29	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
30	chr6:29988600-30009800	Weak transcription	Left Ventricle	heart
31	chr6:29988600-30022200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:29988600-30027400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:29988800-30022800	Weak transcription	Brain Hippocampus Middle	brain
34	chr6:29989000-30009800	Weak transcription	GM12878-XiMat	blood
35	chr6:29989000-30023000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr6:29989400-30021400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:29996600-30012200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr6:29998400-30012200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:29998400-30012200	Weak transcription	HMEC	breast
41	chr6:29999200-30027200	Weak transcription	Fetal Heart	heart
42	chr6:29999800-30012400	Weak transcription	Hela-S3	cervix
43	chr6:29999800-30022200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:30000000-30027400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr6:30001200-30025000	Weak transcription	Fetal Lung	lung
46	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
47	chr6:30001400-30012000	Weak transcription	HSMM	muscle
48	chr6:30001600-30022600	Weak transcription	Brain Substantia Nigra	brain
49	chr6:30001800-30012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:30001800-30014800	Weak transcription	Monocytes-CD14+_RO01746	blood

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