Variant report

Variant	rs13162626
Chromosome Location	chr5:36938041-36938042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:36937263..36939579-chr5:36939659..36941382,2	MCF-7	breast:
2	chr5:36874459..36876976-chr5:36936493..36938823,2	K562	blood:
3	chr5:36935171..36938055-chr5:36942349..36945199,2	MCF-7	breast:
4	chr5:36937606..36940951-chr5:36941936..36944746,3	K562	blood:
5	chr5:36906209..36908902-chr5:36936450..36938338,2	K562	blood:
6	chr5:36926669..36929078-chr5:36937999..36941125,3	MCF-7	breast:
7	chr5:36875949..36878043-chr5:36936778..36939206,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs13156908	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13163996	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13164726	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13165105	0.88[EUR][1000 genomes]
rs13176635	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181330	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13181860	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13186745	0.90[EUR][1000 genomes]
rs13187028	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1353256	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16903418	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17312211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs187391	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs188383	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs213513	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs289216	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293753	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293754	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293775	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298973	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34079524	0.90[EUR][1000 genomes]
rs34218486	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34272373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34697946	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34807025	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34911537	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35127161	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35167018	0.92[EUR][1000 genomes]
rs35357341	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35394109	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35809470	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36035695	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36676	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs3776594	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3899482	0.88[EUR][1000 genomes]
rs58123624	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62654860	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6868809	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6894622	0.90[EUR][1000 genomes]
rs71617772	0.92[EUR][1000 genomes]
rs71617774	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73093888	0.90[EUR][1000 genomes]
rs7700441	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7704442	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716192	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs923957	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv830264	chr5:36887002-36941494	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	nsv1033562	chr5:36927652-36994811	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv1023362	chr5:36927652-37010749	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
11	nsv1017947	chr5:36927652-37017180	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
12	nsv1029936	chr5:36927652-37025871	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
13	nsv1029319	chr5:36928654-37017180	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
14	nsv1030883	chr5:36932448-37039857	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
15	esv1803659	chr5:36935129-37039857	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13162626	C5orf42	cis	cerebellum	SCAN
rs13162626	IL7R	cis	cerebellum	SCAN
rs13162626	TARS	cis	cerebellum	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36907400-36938200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:36919600-36938200	Weak transcription	Pancreas	Pancrea
3	chr5:36919800-36953000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:36919800-36961600	Weak transcription	K562	blood
5	chr5:36920400-36951400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:36923600-36943600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:36924600-36943600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr5:36924800-36939000	Weak transcription	Fetal Thymus	thymus
9	chr5:36924800-36955200	Weak transcription	Dnd41	blood
10	chr5:36926600-36939400	Weak transcription	Fetal Intestine Small	intestine
11	chr5:36927600-36961600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:36929600-36947400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:36929800-36939400	Weak transcription	Osteobl	bone
14	chr5:36930000-36945000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:36930800-36940000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr5:36931200-36939400	Weak transcription	Hela-S3	cervix
17	chr5:36931800-36938200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr5:36931800-36938400	Weak transcription	Ovary	ovary
19	chr5:36932200-36940000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr5:36932200-36940000	Weak transcription	Brain Angular Gyrus	brain
21	chr5:36932400-36943200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:36933200-36940200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:36933200-36944000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:36933200-36962000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:36933400-36949600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:36934600-36941000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr5:36935200-36939000	Weak transcription	HUVEC	blood vessel
28	chr5:36935200-36939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr5:36935200-36947200	Weak transcription	Primary T cells from cord blood	blood
30	chr5:36935400-36938400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:36935600-36938200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:36935600-36938200	Weak transcription	Psoas Muscle	Psoas
33	chr5:36936000-36938800	Weak transcription	Small Intestine	intestine
34	chr5:36936000-36939800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr5:36936000-36951600	Weak transcription	Primary B cells from cord blood	blood
36	chr5:36936200-36938200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:36936200-36940000	Weak transcription	Brain Anterior Caudate	brain
38	chr5:36936200-36944000	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:36936600-36938400	Enhancers	Fetal Heart	heart
40	chr5:36936800-36938200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr5:36936800-36938200	Weak transcription	HepG2	liver
42	chr5:36936800-36939000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr5:36936800-36939800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:36936800-36940000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:36936800-36951000	Weak transcription	Right Ventricle	heart
46	chr5:36937000-36940000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:36937200-36938200	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr5:36937200-36939000	Enhancers	Liver	Liver
49	chr5:36937400-36938200	Enhancers	Brain Hippocampus Middle	brain
50	chr5:36937400-36938400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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