Variant report

Variant	rs9729395
Chromosome Location	chr1:45975166-45975167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:45974939..45977846-chr1:46015282..46017928,2	MCF-7	breast:
2	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
3	chr1:45974971..45980027-chr1:46048272..46053531,9	K562	blood:
4	chr1:45965671..45969478-chr1:45972057..45975317,5	MCF-7	breast:
5	chr1:45805983..45807549-chr1:45973532..45975768,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AKR1A1-3	chr1:45975105-45975180	NONHSAT002944

Variant related genes	Relation type
ENSG00000132781	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000117448	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1006216	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1007858	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10789464	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890330	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11211111	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11211117	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211118	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11211123	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211128	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037201	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12042903	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046816	0.81[EUR][1000 genomes]
rs12066142	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12067642	0.90[EUR][1000 genomes]
rs12097497	0.81[EUR][1000 genomes]
rs12410493	0.83[EUR][1000 genomes]
rs12564806	0.88[EUR][1000 genomes]
rs1494812	0.81[EUR][1000 genomes]
rs1826691	0.81[EUR][1000 genomes]
rs2055145	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2088100	0.81[EUR][1000 genomes]
rs28555082	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2883968	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34673142	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790582	0.81[EUR][1000 genomes]
rs3790583	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4633317	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4660855	0.81[EUR][1000 genomes]
rs4660858	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4660863	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55642258	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61788261	0.82[EUR][1000 genomes]
rs61788281	0.84[EUR][1000 genomes]
rs61788285	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61788336	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788356	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67683090	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713358	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528573	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs868351	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9727262	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
9	nsv932954	chr1:45975022-45976755	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9729395	C2orf49	trans	lymphoblastoid	RTeQTL
rs9729395	PRDX1	cis	Thyroid	GTEx
rs9729395	TESK2	cis	Whole Blood	GTEx
rs9729395	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45966400-45975600	Weak transcription	HSMMtube	muscle
2	chr1:45966400-45975800	Weak transcription	Aorta	Aorta
3	chr1:45966600-45984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:45966800-45975800	Weak transcription	HSMM	muscle
5	chr1:45966800-45975800	Weak transcription	NHDF-Ad	bronchial
6	chr1:45966800-45976000	Weak transcription	Fetal Brain Male	brain
7	chr1:45966800-45976000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:45966800-45980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:45967000-45975400	Weak transcription	NH-A	brain
11	chr1:45967000-45975600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr1:45967000-45975800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:45967000-45977200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:45967200-45975200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:45967200-45975400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:45967200-45975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:45967200-45975600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:45967200-45975600	Weak transcription	Psoas Muscle	Psoas
19	chr1:45967200-45975800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:45967200-45976200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:45967200-45976200	Weak transcription	Fetal Lung	lung
22	chr1:45967400-45975600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:45967400-45975800	Weak transcription	Stomach Mucosa	stomach
24	chr1:45971600-45985000	Strong transcription	Fetal Stomach	stomach
25	chr1:45971800-45980400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:45971800-45982000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr1:45972800-45978200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:45972800-45978400	Strong transcription	Fetal Intestine Small	intestine
29	chr1:45972800-45980400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:45972800-45982200	Strong transcription	K562	blood
31	chr1:45972800-45982400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:45972800-45984400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr1:45972800-45984400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:45972800-45984400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr1:45972800-45984600	Strong transcription	Fetal Thymus	thymus
36	chr1:45973000-45976800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:45973000-45981800	Strong transcription	Dnd41	blood
38	chr1:45973000-45983000	Strong transcription	Fetal Brain Female	brain
39	chr1:45973000-45983200	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr1:45973000-45983200	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:45973000-45983400	Strong transcription	Primary B cells from peripheral blood	blood
42	chr1:45973000-45983800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr1:45973000-45983800	Strong transcription	Spleen	Spleen
44	chr1:45973000-45984000	Strong transcription	Primary T cells from cord blood	blood
45	chr1:45973000-45984000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:45973000-45984000	Strong transcription	Fetal Muscle Leg	muscle
47	chr1:45973000-45984400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr1:45973000-45984400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:45973000-45984600	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr1:45973200-45975800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

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