Variant report

Variant	rs12200607
Chromosome Location	chr6:146122137-146122138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:146120708..146122690-chr6:146126076..146128209,2	MCF-7	breast:
2	chr6:146117599..146120240-chr6:146121870..146124861,2	MCF-7	breast:
3	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:
4	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: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10447450	0.91[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs10457789	0.91[CEU][hapmap]
rs12193627	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12195117	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs12195987	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12198683	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12205454	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12212636	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12214668	0.91[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs12214705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13196875	0.84[EUR][1000 genomes]
rs13200495	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs13201738	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13203662	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13209322	0.91[CEU][hapmap]
rs13210966	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17225973	0.91[CEU][hapmap]
rs28703599	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34211445	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35587488	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35667536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35807318	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811105	1.00[AFR][1000 genomes]
rs3923580	0.91[CEU][hapmap]
rs73579446	0.87[EUR][1000 genomes]
rs952407	0.82[EUR][1000 genomes]

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:110 , 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	chr6:146106600-146122200	Weak transcription	NHLF	lung
9	chr6:146106800-146122800	Weak transcription	HSMMtube	muscle
10	chr6:146107000-146122200	Weak transcription	Left Ventricle	heart
11	chr6:146107000-146125600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr6:146110200-146135000	Weak transcription	Pancreas	Pancrea
13	chr6:146112400-146122200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr6:146112400-146122400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:146112400-146122400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr6:146112400-146122400	Weak transcription	Adipose Nuclei	Adipose
17	chr6:146112400-146123000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:146112400-146125400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr6:146112400-146125400	Weak transcription	Fetal Stomach	stomach
20	chr6:146112400-146125600	Weak transcription	Aorta	Aorta
21	chr6:146112400-146125600	Weak transcription	Brain Substantia Nigra	brain
22	chr6:146112400-146135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:146112600-146122200	Weak transcription	Primary B cells from cord blood	blood
24	chr6:146112600-146124600	Weak transcription	Liver	Liver
25	chr6:146112600-146125800	Weak transcription	Fetal Brain Female	brain
26	chr6:146113000-146123200	Weak transcription	HMEC	breast
27	chr6:146113200-146122200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr6:146113200-146122800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:146113400-146122800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:146113400-146133600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:146113600-146122200	Weak transcription	Psoas Muscle	Psoas
32	chr6:146113600-146122800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:146113800-146124000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:146113800-146126000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:146114200-146122200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:146114200-146122200	Weak transcription	A549	lung
37	chr6:146114200-146123000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:146114400-146123200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:146114400-146125400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:146114600-146122400	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:146114600-146122800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr6:146116400-146126600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:146116600-146123200	Weak transcription	Fetal Lung	lung
44	chr6:146116600-146124600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:146116800-146123200	Weak transcription	Fetal Intestine Large	intestine
46	chr6:146116800-146125400	Weak transcription	Esophagus	oesophagus
47	chr6:146116800-146126400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr6:146116800-146128600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:146117200-146126200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr6:146117400-146130400	Strong transcription	HSMM	muscle

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