Variant report

Variant	rs999860
Chromosome Location	chr6:146122753-146122754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146117599..146120240-chr6:146121870..146124861,2	MCF-7	breast:
2	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:
3	chr6:146121190..146123447-chr6:146128257..146129853,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000270828	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000112425	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17223456	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821586	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821684	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17821702	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17822170	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856245	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1935614	1.00[ASN][1000 genomes]
rs1988640	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068029	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28568954	1.00[ASN][1000 genomes]
rs3891273	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4343934	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895680	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895681	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4895685	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895686	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896823	1.00[ASN][1000 genomes]
rs4896825	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4896830	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4896834	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4896845	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896846	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4896849	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56241331	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58588227	1.00[ASN][1000 genomes]
rs60043524	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61041405	1.00[ASN][1000 genomes]
rs6570721	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6570722	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914746	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6920248	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6921551	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938028	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7341315	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs734166	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73568138	1.00[ASN][1000 genomes]
rs73570014	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73579478	1.00[ASN][1000 genomes]
rs9497352	1.00[ASN][1000 genomes]
rs9497355	1.00[ASN][1000 genomes]
rs9497366	1.00[ASN][1000 genomes]
rs9497368	1.00[ASN][1000 genomes]
rs9767028	1.00[ASN][1000 genomes]
rs999859	1.00[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146100600-146123200	Weak transcription	HUVEC	blood vessel
2	chr6:146104600-146127000	Weak transcription	Brain Hippocampus Middle	brain
3	chr6:146105000-146123200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:146105200-146134400	Weak transcription	Thymus	Thymus
5	chr6:146105400-146125800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:146105800-146125600	Weak transcription	Fetal Kidney	kidney
7	chr6:146106000-146133600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:146106800-146122800	Weak transcription	HSMMtube	muscle
9	chr6:146107000-146125600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:146110200-146135000	Weak transcription	Pancreas	Pancrea
11	chr6:146112400-146123000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:146112400-146125400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr6:146112400-146125400	Weak transcription	Fetal Stomach	stomach
14	chr6:146112400-146125600	Weak transcription	Aorta	Aorta
15	chr6:146112400-146125600	Weak transcription	Brain Substantia Nigra	brain
16	chr6:146112400-146135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:146112600-146124600	Weak transcription	Liver	Liver
18	chr6:146112600-146125800	Weak transcription	Fetal Brain Female	brain
19	chr6:146113000-146123200	Weak transcription	HMEC	breast
20	chr6:146113200-146122800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:146113400-146122800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr6:146113400-146133600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr6:146113600-146122800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:146113800-146124000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:146113800-146126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:146114200-146123000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:146114400-146123200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:146114400-146125400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:146114600-146122800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:146116400-146126600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:146116600-146123200	Weak transcription	Fetal Lung	lung
32	chr6:146116600-146124600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:146116800-146123200	Weak transcription	Fetal Intestine Large	intestine
34	chr6:146116800-146125400	Weak transcription	Esophagus	oesophagus
35	chr6:146116800-146126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:146116800-146128600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:146117200-146126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:146117400-146130400	Strong transcription	HSMM	muscle
39	chr6:146118000-146125600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:146118400-146126400	Weak transcription	Spleen	Spleen
41	chr6:146118400-146128600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:146118800-146122800	Weak transcription	Placenta	Placenta
43	chr6:146118800-146124800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:146118800-146125600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:146119000-146123200	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:146119000-146125600	Weak transcription	Brain Anterior Caudate	brain
47	chr6:146119000-146126200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr6:146119200-146125600	Weak transcription	Ovary	ovary
49	chr6:146119200-146134800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr6:146119400-146126400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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