Variant report

Variant	rs2639703
Chromosome Location	chr1:225812911-225812912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225798398..225800029-chr1:225812208..225813908,2	MCF-7	breast:
2	chr1:225812132..225816261-chr1:225840645..225843021,5	MCF-7	breast:
3	chr1:225812743..225815583-chr1:225838779..225842082,3	MCF-7	breast:
4	chr1:225811629..225814682-chr1:225837317..225840214,3	MCF-7	breast:
5	chr1:225812888..225814596-chr1:225815974..225818841,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10753406	0.83[EUR][1000 genomes]
rs1075364	0.81[LWK][hapmap]
rs10799316	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap]
rs10799317	0.82[EUR][1000 genomes]
rs10799318	0.83[EUR][1000 genomes]
rs10799319	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10915828	0.93[CHB][hapmap];0.81[CHD][hapmap]
rs10915833	0.83[EUR][1000 genomes]
rs10915834	0.81[EUR][1000 genomes]
rs10915839	0.82[EUR][1000 genomes]
rs10915847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11584675	0.83[EUR][1000 genomes]
rs12028305	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs2639712	0.89[TSI][hapmap]
rs2639716	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2657564	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2657569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2840958	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2840967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2840968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3820226	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3856156	0.83[EUR][1000 genomes]
rs4653643	0.95[CEU][hapmap];0.94[CHB][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs476540	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs487591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs498350	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs510293	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs511649	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs516249	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs551996	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554992	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561656	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs576861	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6426076	0.83[EUR][1000 genomes]
rs6668770	0.83[EUR][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs6751	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs712062	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7515907	0.83[EUR][1000 genomes]
rs7524766	0.83[EUR][1000 genomes]
rs7540181	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7541598	0.83[EUR][1000 genomes]
rs7555139	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7555553	0.83[EUR][1000 genomes]
rs9804142	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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2639703	ENAH	cis	normal skin	skin_eQTL
rs2639703	C1orf55	cis	parietal	SCAN
rs2639703	RP11-496N12.9	cis	Thyroid	GTEx
rs2639703	C1orf58	cis	parietal	SCAN
rs2639703	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
4	chr1:225793600-225813200	Weak transcription	Left Ventricle	heart
5	chr1:225793600-225813800	Weak transcription	NH-A	brain
6	chr1:225794600-225813200	Weak transcription	Lung	lung
7	chr1:225795600-225813200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:225795600-225813200	Weak transcription	Psoas Muscle	Psoas
9	chr1:225795600-225813800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:225797200-225815200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:225797400-225814000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:225801600-225813600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:225802600-225813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:225802600-225813800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:225805800-225814800	Weak transcription	Duodenum Mucosa	Duodenum
16	chr1:225806000-225813400	Weak transcription	Aorta	Aorta
17	chr1:225806000-225813800	Weak transcription	Fetal Intestine Small	intestine
18	chr1:225806200-225817600	Weak transcription	Fetal Brain Female	brain
19	chr1:225806400-225813400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:225806400-225813800	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:225806400-225814200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:225806400-225814200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:225806400-225814400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:225806400-225815200	Weak transcription	Adipose Nuclei	Adipose
25	chr1:225806800-225813200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:225806800-225813200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:225806800-225813600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr1:225806800-225813800	Weak transcription	Right Ventricle	heart
29	chr1:225806800-225814000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:225806800-225814000	Weak transcription	NHDF-Ad	bronchial
31	chr1:225806800-225814600	Weak transcription	A549	lung
32	chr1:225807000-225814000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr1:225807200-225813200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:225807200-225820400	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:225808200-225818400	Weak transcription	Fetal Brain Male	brain
36	chr1:225809600-225813000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:225809600-225813600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr1:225810000-225813600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:225810000-225825400	Weak transcription	NHEK	skin
41	chr1:225810600-225813200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:225810600-225813600	Weak transcription	Brain Substantia Nigra	brain
43	chr1:225810600-225813600	Weak transcription	HSMM	muscle
44	chr1:225810600-225815000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:225810600-225815200	Weak transcription	Pancreas	Pancrea
46	chr1:225810600-225815600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:225810800-225813800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:225812400-225813000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:225812400-225814000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:225812400-225815800	Enhancers	Fetal Lung	lung

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