Variant report

Variant	rs7529229
Chromosome Location	chr1:154420778-154420779
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154377400..154379545-chr1:154419096..154421109,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228013	Chromatin interaction
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11265613	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12126142	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133641	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12730036	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12730935	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12753254	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228145	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4129267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4393147	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4453032	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4537545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4576655	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845371	0.88[ASW][hapmap]
rs4845372	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845373	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845620	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4845621	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845622	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845623	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845625	0.94[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes]
rs56383622	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61812598	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427658	0.81[ASW][hapmap]
rs6664201	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6684439	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[ASN][1000 genomes]
rs6689393	0.94[ASW][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes]
rs6694258	0.82[AFR][1000 genomes]
rs6694817	0.88[ASW][hapmap]
rs7512646	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518199	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7521458	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7529229	ANXA9	cis	parietal	SCAN
rs7529229	LYSMD1	cis	cerebellum	SCAN
rs7529229	LINGO4	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154403200-154426000	Weak transcription	Brain Angular Gyrus	brain
2	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
5	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
8	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
9	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
10	chr1:154412800-154425800	Weak transcription	HepG2	liver
11	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:154414400-154424400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:154414400-154424400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:154414600-154424400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:154414600-154426000	Weak transcription	Thymus	Thymus
16	chr1:154414800-154436000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:154415200-154420800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:154415200-154424000	Weak transcription	Fetal Stomach	stomach
19	chr1:154415800-154425800	Weak transcription	Esophagus	oesophagus
20	chr1:154416200-154435800	Strong transcription	Liver	Liver
21	chr1:154416600-154420800	Weak transcription	Right Ventricle	heart
22	chr1:154416600-154424400	Weak transcription	Colonic Mucosa	Colon
23	chr1:154416600-154425600	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr1:154417400-154428000	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:154417800-154422000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:154417800-154426000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:154418000-154425600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:154418000-154425800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:154418000-154428000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
31	chr1:154418200-154425000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:154418600-154420800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:154418600-154425400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:154418600-154432800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr1:154418800-154420800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:154418800-154425800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:154419000-154420800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr1:154419000-154424400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:154419000-154425000	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr1:154419200-154425200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:154419200-154425400	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:154419200-154425600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:154419200-154425800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:154419200-154425800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:154419200-154427200	Weak transcription	Ovary	ovary
46	chr1:154419200-154432200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:154419200-154435800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:154419400-154423200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:154419400-154425600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:154419600-154422600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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