Variant report

Variant	rs6664201
Chromosome Location	chr1:154414296-154414297
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154401786..154404532-chr1:154413417..154415203,2	K562	blood:
2	chr1:154413948..154418058-chr1:154421616..154424516,3	MCF-7	breast:
3	chr1:154406170..154408032-chr1:154413568..154416064,2	MCF-7	breast:
4	chr1:154410246..154412652-chr1:154413063..154415706,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11265613	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12126142	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12133641	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12730036	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730935	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12753254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228145	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4129267	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133213	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4393147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4537545	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4576655	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845372	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845373	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845620	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4845621	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845622	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56383622	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61812598	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6684439	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7512646	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518199	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7521458	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7529229	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]

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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6664201	GPATCH4	cis	cerebellum	SCAN
rs6664201	LINGO4	cis	parietal	SCAN

Chromatin state (count:96 , 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	chr1:154403800-154417600	Weak transcription	Small Intestine	intestine
3	chr1:154406000-154423200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:154406200-154417600	Weak transcription	Hela-S3	cervix
5	chr1:154406200-154425600	Weak transcription	Primary B cells from cord blood	blood
6	chr1:154407400-154414400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:154407400-154414600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:154407400-154416200	Genic enhancers	Liver	Liver
9	chr1:154407400-154417400	Weak transcription	Brain Anterior Caudate	brain
10	chr1:154407600-154417200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:154407600-154418600	Weak transcription	Ovary	ovary
12	chr1:154408600-154414400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:154408600-154414800	Strong transcription	Skeletal Muscle Female	skeletal muscle
14	chr1:154408600-154420600	Weak transcription	Brain Hippocampus Middle	brain
15	chr1:154408600-154425800	Weak transcription	Brain Substantia Nigra	brain
16	chr1:154408800-154416000	Weak transcription	Right Ventricle	heart
17	chr1:154408800-154420600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:154408800-154420600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:154408800-154421000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:154408800-154425600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:154409200-154417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:154409200-154420600	Weak transcription	Gastric	stomach
23	chr1:154409200-154425800	Weak transcription	Right Atrium	heart
24	chr1:154409400-154424600	Weak transcription	Stomach Mucosa	stomach
25	chr1:154410400-154414400	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:154410400-154418000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:154410600-154414400	Genic enhancers	Monocytes-CD14+_RO01746	blood
28	chr1:154410600-154415800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr1:154410800-154418600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:154410800-154418800	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:154411000-154415600	Strong transcription	Stomach Smooth Muscle	stomach
32	chr1:154411400-154416000	Weak transcription	Left Ventricle	heart
33	chr1:154411600-154415400	Weak transcription	Colonic Mucosa	Colon
34	chr1:154412000-154414400	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr1:154412400-154415800	Enhancers	Fetal Thymus	thymus
36	chr1:154412600-154415600	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr1:154412600-154425800	Weak transcription	Psoas Muscle	Psoas
38	chr1:154412800-154414800	Enhancers	GM12878-XiMat	blood
39	chr1:154412800-154415600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:154412800-154417000	Weak transcription	Fetal Intestine Small	intestine
41	chr1:154412800-154425800	Weak transcription	HepG2	liver
42	chr1:154413000-154414600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr1:154413000-154419600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:154413200-154415000	Enhancers	Esophagus	oesophagus
45	chr1:154413200-154422600	Weak transcription	Primary B cells from peripheral blood	blood
46	chr1:154413400-154414400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr1:154413400-154415000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr1:154413400-154415000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:154413400-154415200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr1:154413400-154415800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood

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