Variant report

Variant	rs7544225
Chromosome Location	chr1:212409008-212409009
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	chr1:212408314..212411280-chr1:212781747..212784026,2	K562	blood:

Variant related genes	Relation type
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10019	0.96[CEU][hapmap]
rs1009622	1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs11119884	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs11119885	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs11119887	0.89[ASN][1000 genomes]
rs11119904	0.83[EUR][1000 genomes]
rs12033246	0.96[CEU][hapmap]
rs12035647	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs12036130	0.86[EUR][1000 genomes]
rs12402397	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1389369	0.83[CHB][hapmap];0.82[ASN][1000 genomes]
rs1389370	0.83[ASN][1000 genomes]
rs1389371	1.00[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1472226	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs17042034	0.83[EUR][1000 genomes]
rs1774249	0.92[CEU][hapmap]
rs1967116	0.82[ASN][1000 genomes]
rs1967117	0.84[ASN][1000 genomes]
rs1992643	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2001234	0.86[ASN][1000 genomes]
rs2012917	0.83[CHB][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs2087946	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs2252044	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs2307128	0.83[ASN][1000 genomes]
rs2516331	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2589474	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2884512	0.84[ASN][1000 genomes]
rs3099112	0.96[CEU][hapmap]
rs351373	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351377	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351378	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351379	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351380	0.82[EUR][1000 genomes]
rs351386	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs351393	0.96[CEU][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs351398	0.81[EUR][1000 genomes]
rs351401	0.83[EUR][1000 genomes]
rs351407	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs351408	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351417	0.86[EUR][1000 genomes]
rs351419	0.89[EUR][1000 genomes]
rs35209719	0.82[ASN][1000 genomes]
rs3767861	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs3767862	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs3816912	0.81[ASN][1000 genomes]
rs4362041	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs4951581	0.82[ASN][1000 genomes]
rs4951582	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951589	0.96[CEU][hapmap]
rs6540731	0.91[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6540732	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6540733	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs6540734	0.83[ASN][1000 genomes]
rs6540735	0.83[ASN][1000 genomes]
rs6657900	0.83[CHB][hapmap];0.83[ASN][1000 genomes]
rs6668866	0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs6679796	0.91[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7415843	0.96[CEU][hapmap]
rs7511781	0.83[ASN][1000 genomes]
rs7515645	0.83[ASN][1000 genomes]
rs7518329	0.80[ASN][1000 genomes]
rs7519168	0.91[CHB][hapmap];0.84[ASN][1000 genomes]
rs7519959	0.96[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs7542973	0.80[ASN][1000 genomes]
rs867584	0.85[ASN][1000 genomes]
rs903120	0.84[ASN][1000 genomes]
rs903121	0.83[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs951623	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7544225	TMEM206	cis	cerebellum	SCAN
rs7544225	LGTN	cis	cerebellum	SCAN
rs7544225	SLC30A1	cis	cerebellum	SCAN
rs7544225	SYT14	cis	cerebellum	SCAN
rs7544225	CD34	cis	cerebellum	SCAN
rs7544225	TMEM206	cis	parietal	SCAN
rs7544225	TMEM206	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212403600-212409600	Weak transcription	Liver	Liver
2	chr1:212404800-212410800	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr1:212405200-212410600	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr1:212405600-212414800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:212405600-212416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:212406400-212411000	Enhancers	HSMMtube	muscle
7	chr1:212406600-212409200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr1:212406600-212410800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:212406800-212409800	Enhancers	Fetal Muscle Leg	muscle
10	chr1:212406800-212410400	Enhancers	HSMM	muscle
11	chr1:212406800-212410600	Enhancers	Stomach Mucosa	stomach
12	chr1:212407000-212409200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:212407200-212410400	Enhancers	Left Ventricle	heart
14	chr1:212407600-212409200	Enhancers	NHLF	lung
15	chr1:212407600-212410000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:212407600-212412400	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:212407800-212409600	Enhancers	Right Atrium	heart
18	chr1:212407800-212409800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:212407800-212410400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr1:212407800-212412800	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr1:212408000-212409200	Weak transcription	Right Ventricle	heart
22	chr1:212408000-212410600	Enhancers	Fetal Heart	heart
23	chr1:212408000-212411600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:212408000-212411800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:212408000-212413000	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr1:212408200-212409600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr1:212408200-212409800	Enhancers	Small Intestine	intestine
28	chr1:212408200-212415400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:212408400-212409800	Enhancers	Lung	lung
30	chr1:212408400-212410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:212408400-212411600	Weak transcription	Primary hematopoietic stem cells	blood
32	chr1:212408400-212415600	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:212408600-212409200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:212408600-212409200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:212408600-212409400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:212408600-212409400	Weak transcription	Psoas Muscle	Psoas
37	chr1:212408600-212409600	Weak transcription	Colonic Mucosa	Colon
38	chr1:212408600-212410200	Weak transcription	HepG2	liver
39	chr1:212408600-212410400	Weak transcription	HMEC	breast
40	chr1:212408600-212410800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:212408600-212410800	Weak transcription	GM12878-XiMat	blood
42	chr1:212408600-212411000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:212408600-212411000	Weak transcription	NHDF-Ad	bronchial
44	chr1:212408600-212411200	Weak transcription	A549	lung
45	chr1:212408600-212411600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:212408600-212411600	Weak transcription	Adipose Nuclei	Adipose
47	chr1:212408600-212411600	Weak transcription	Brain Anterior Caudate	brain
48	chr1:212408600-212411600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:212408600-212411600	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:212408600-212411600	Weak transcription	Rectal Smooth Muscle	rectum

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