Variant report

Variant	rs3008613
Chromosome Location	chr1:222795769-222795770
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222791253..222793444-chr1:222793463..222795812,3	MCF-7	breast:
2	chr1:222713330..222714959-chr1:222794373..222797061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143512	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1053316	0.85[JPT][hapmap]
rs1986348	1.00[EUR][1000 genomes]
rs2291833	0.84[ASN][1000 genomes]
rs2936019	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2936024	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2936025	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936026	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2936056	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2936057	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002137	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002138	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002140	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002150	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008599	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008600	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008603	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008605	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3008611	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3008620	0.88[ASN][1000 genomes]
rs3008624	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008627	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008628	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008632	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3008633	0.85[JPT][hapmap]
rs3008634	0.85[JPT][hapmap]
rs3008635	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3008639	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]
rs34290674	0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34851033	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35684750	0.85[JPT][hapmap]
rs35762933	0.85[JPT][hapmap]
rs4379681	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73124815	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73124822	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73124862	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73124880	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124889	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124891	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73126803	1.00[EUR][1000 genomes]
rs73126812	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73126814	0.80[AMR][1000 genomes];1.00[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3008613	ESPNL	trans	brain	seeQTL
rs3008613	COMP	trans	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222800000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:222792600-222801400	Weak transcription	Lung	lung
4	chr1:222792600-222802200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:222792600-222802200	Weak transcription	Aorta	Aorta
6	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:222792800-222796000	Weak transcription	Brain Germinal Matrix	brain
9	chr1:222792800-222796200	Weak transcription	A549	lung
10	chr1:222792800-222802000	Weak transcription	Colonic Mucosa	Colon
11	chr1:222793000-222796000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:222793000-222796200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:222793000-222797000	Weak transcription	Fetal Intestine Large	intestine
14	chr1:222793000-222798800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:222793000-222799000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:222793000-222799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:222793000-222800200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:222793000-222802200	Weak transcription	HSMMtube	muscle
19	chr1:222793200-222795800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr1:222793200-222795800	Weak transcription	Brain Anterior Caudate	brain
21	chr1:222793200-222796000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:222793200-222796000	Weak transcription	Placenta	Placenta
23	chr1:222793200-222796200	Weak transcription	Primary B cells from cord blood	blood
24	chr1:222793200-222796200	Weak transcription	Fetal Brain Female	brain
25	chr1:222793200-222796800	Weak transcription	Fetal Heart	heart
26	chr1:222793200-222797600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:222793200-222797800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:222793200-222797800	Weak transcription	Fetal Lung	lung
29	chr1:222793200-222797800	Weak transcription	HUVEC	blood vessel
30	chr1:222793200-222798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:222793200-222799400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:222793200-222799400	Weak transcription	Thymus	Thymus
33	chr1:222793200-222800000	Weak transcription	Pancreas	Pancrea
34	chr1:222793200-222800000	Weak transcription	Spleen	Spleen
35	chr1:222793200-222800000	Weak transcription	HMEC	breast
36	chr1:222793200-222800000	Weak transcription	NHLF	lung
37	chr1:222793200-222800200	Weak transcription	NHEK	skin
38	chr1:222793200-222800400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:222793200-222801000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr1:222793200-222801400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:222793200-222802200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:222793200-222802200	Weak transcription	Fetal Intestine Small	intestine
43	chr1:222793200-222802200	Weak transcription	Right Ventricle	heart
44	chr1:222793200-222802800	Weak transcription	Gastric	stomach
45	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
47	chr1:222793400-222796000	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:222793400-222796200	Weak transcription	Osteobl	bone
49	chr1:222793400-222800000	Weak transcription	Brain Substantia Nigra	brain
50	chr1:222793600-222796000	Weak transcription	Rectal Mucosa Donor 31	rectum

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