Variant report

Variant	rs2840967
Chromosome Location	chr1:225824028-225824029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225821477..225824756-chr1:225839362..225842752,3	MCF-7	breast:
2	chr1:225823843..225826743-chr1:225847981..225850951,2	K562	blood:
3	chr1:225821970..225824548-chr1:226027169..226028727,2	K562	blood:
4	chr1:225823441..225825112-chr1:225825281..225827409,2	K562	blood:
5	chr1:225823669..225825738-chr1:225832023..225834432,2	MCF-7	breast:
6	chr1:225820712..225822349-chr1:225823741..225825901,2	K562	blood:

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:46)

rs_ID	r²[population]
rs10753406	0.81[EUR][1000 genomes]
rs1075364	0.82[LWK][hapmap]
rs10799316	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap]
rs10799317	0.81[EUR][1000 genomes]
rs10799318	0.82[EUR][1000 genomes]
rs10799319	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs10915828	0.93[CHB][hapmap]
rs10915833	0.81[EUR][1000 genomes]
rs10915839	0.81[EUR][1000 genomes]
rs10915847	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11584675	0.81[EUR][1000 genomes]
rs12028305	0.82[EUR][1000 genomes]
rs1222440	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs2639703	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]
rs2639712	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs2639716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657564	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2657569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2840958	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2840968	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3820226	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs3856156	0.81[EUR][1000 genomes]
rs4653643	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs476540	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs487591	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs498350	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs510293	0.84[EUR][1000 genomes]
rs511649	0.88[EUR][1000 genomes]
rs516249	0.87[EUR][1000 genomes]
rs551996	0.84[EUR][1000 genomes]
rs554744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs554992	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs561656	0.91[EUR][1000 genomes]
rs576861	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs6426076	0.81[EUR][1000 genomes]
rs6668770	0.81[EUR][1000 genomes]
rs6697783	0.94[CHB][hapmap];0.81[CHD][hapmap]
rs6751	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs712062	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs7515907	0.81[EUR][1000 genomes]
rs7524766	0.81[EUR][1000 genomes]
rs7540181	0.83[EUR][1000 genomes]
rs7541598	0.81[EUR][1000 genomes]
rs7555139	0.83[EUR][1000 genomes]
rs7555553	0.81[EUR][1000 genomes]
rs9804142	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2840967	ENAH	cis	normal skin	skin_eQTL
rs2840967	C1orf58	cis	parietal	SCAN
rs2840967	RP11-496N12.9	cis	Thyroid	GTEx
rs2840967	C1orf55	cis	parietal	SCAN
rs2840967	MIXL1	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
2	chr1:225809800-225837800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:225810000-225825400	Weak transcription	NHEK	skin
4	chr1:225812800-225824400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:225812800-225825000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr1:225813400-225824800	Weak transcription	Lung	lung
7	chr1:225813600-225837600	Weak transcription	HUVEC	blood vessel
8	chr1:225813800-225838600	Weak transcription	HMEC	breast
9	chr1:225814400-225825200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:225814400-225825400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:225814600-225835800	Weak transcription	HSMMtube	muscle
12	chr1:225815600-225825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:225815600-225830000	Weak transcription	Pancreas	Pancrea
14	chr1:225815800-225825400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:225815800-225839000	Weak transcription	Fetal Intestine Large	intestine
16	chr1:225816000-225825600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:225816000-225825800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:225816000-225825800	Weak transcription	HepG2	liver
19	chr1:225816000-225830000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:225816000-225832400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:225816000-225834200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:225816000-225838400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:225816000-225838600	Weak transcription	Fetal Kidney	kidney
24	chr1:225816200-225835400	Weak transcription	Fetal Heart	heart
25	chr1:225816200-225836000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr1:225816200-225836600	Weak transcription	Adipose Nuclei	Adipose
27	chr1:225816800-225832000	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:225817000-225825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:225817000-225825400	Weak transcription	Brain Germinal Matrix	brain
30	chr1:225817200-225834000	Weak transcription	Psoas Muscle	Psoas
31	chr1:225818800-225825800	Weak transcription	A549	lung
32	chr1:225819000-225831000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:225819000-225832200	Weak transcription	NHDF-Ad	bronchial
34	chr1:225819200-225825400	Weak transcription	Fetal Intestine Small	intestine
35	chr1:225819200-225829600	Weak transcription	Left Ventricle	heart
36	chr1:225819200-225830000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:225819200-225830000	Weak transcription	Gastric	stomach
38	chr1:225819600-225825600	Weak transcription	Fetal Brain Male	brain
39	chr1:225819600-225836400	Weak transcription	Brain Angular Gyrus	brain
40	chr1:225820000-225835800	Weak transcription	Brain Anterior Caudate	brain
41	chr1:225820200-225824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:225820600-225825400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:225820600-225826000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:225820600-225826600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr1:225820800-225829800	Weak transcription	HSMM	muscle
46	chr1:225820800-225837200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr1:225821000-225825200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:225822800-225828200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:225823000-225824400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:225823200-225824400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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