Variant report

Variant	rs3008639
Chromosome Location	chr1:222868412-222868413
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222846053..222848100-chr1:222867819..222869490,2	K562	blood:
2	chr1:222868022..222869542-chr1:222883942..222885819,2	K562	blood:
3	chr1:222850841..222853779-chr1:222868153..222870820,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1053316	0.89[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap]
rs1986348	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2936019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936024	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2936026	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2936056	0.83[EUR][1000 genomes]
rs2936057	0.83[EUR][1000 genomes]
rs3002137	0.83[EUR][1000 genomes]
rs3002138	0.83[EUR][1000 genomes]
rs3002140	0.83[EUR][1000 genomes]
rs3002150	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008599	0.83[EUR][1000 genomes]
rs3008600	0.83[EUR][1000 genomes]
rs3008603	0.83[EUR][1000 genomes]
rs3008605	0.83[EUR][1000 genomes]
rs3008611	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008613	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3008624	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3008627	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008628	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008632	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3008633	0.95[CHD][hapmap];0.85[JPT][hapmap]
rs3008634	0.94[CHD][hapmap];0.85[JPT][hapmap]
rs3008635	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs34290674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34851033	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35684750	0.81[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs35762933	0.81[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs4379681	0.83[EUR][1000 genomes]
rs73124815	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124822	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124862	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73124880	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73124889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73124891	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73126803	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73126812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73126814	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3008639	BROX	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222835200-222884600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:222839000-222877400	Weak transcription	Psoas Muscle	Psoas
3	chr1:222839000-222884600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:222839600-222884600	Weak transcription	Esophagus	oesophagus
5	chr1:222840000-222884600	Weak transcription	Colonic Mucosa	Colon
6	chr1:222841200-222883400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:222841400-222883200	Weak transcription	Fetal Heart	heart
8	chr1:222845000-222884600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:222847800-222872000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:222849200-222875600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:222849400-222875400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:222849400-222883200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:222849600-222877800	Weak transcription	Fetal Brain Female	brain
14	chr1:222852400-222883800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:222854000-222875600	Weak transcription	NHLF	lung
16	chr1:222855200-222884600	Weak transcription	Pancreas	Pancrea
17	chr1:222855400-222873200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:222855600-222883800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:222860000-222884600	Weak transcription	Left Ventricle	heart
20	chr1:222860200-222872400	Weak transcription	K562	blood
21	chr1:222860200-222873200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:222860200-222873400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:222860200-222873800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:222860200-222874400	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:222860200-222875600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:222860200-222875600	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:222860200-222875600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:222860200-222875600	Weak transcription	NHEK	skin
29	chr1:222860200-222877400	Weak transcription	A549	lung
30	chr1:222860200-222883000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:222860200-222883000	Weak transcription	Hela-S3	cervix
32	chr1:222860200-222883200	Weak transcription	Brain Anterior Caudate	brain
33	chr1:222860200-222883600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:222860200-222883800	Weak transcription	Fetal Kidney	kidney
35	chr1:222860200-222884000	Weak transcription	Brain Angular Gyrus	brain
36	chr1:222860200-222884200	Weak transcription	Brain Substantia Nigra	brain
37	chr1:222860200-222884400	Weak transcription	Placenta	Placenta
38	chr1:222860200-222884600	Weak transcription	Aorta	Aorta
39	chr1:222860200-222884600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:222860200-222884600	Weak transcription	Gastric	stomach
41	chr1:222860200-222884600	Weak transcription	Lung	lung
42	chr1:222860400-222872200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:222860400-222872600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr1:222860400-222872600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:222860400-222877600	Weak transcription	HSMMtube	muscle
46	chr1:222860600-222872200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:222860600-222872600	Weak transcription	Brain Germinal Matrix	brain
48	chr1:222860600-222872800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:222860600-222873400	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:222860600-222873400	Weak transcription	Thymus	Thymus

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