Variant report

Variant	rs16903413
Chromosome Location	chr5:36945534-36945535
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:36875293..36878744-chr5:36944693..36947433,6	MCF-7	breast:
2	chr5:36945026..36947869-chr5:36950785..36953502,2	K562	blood:
3	chr5:36877079..36878828-chr5:36943978..36945931,2	MCF-7	breast:
4	chr5:36943731..36946422-chr5:36953381..36955918,2	MCF-7	breast:
5	chr5:36876438..36878732-chr5:36943476..36946469,3	K562	blood:
6	chr5:36943349..36945887-chr5:36955686..36957216,2	K562	blood:
7	chr5:36876324..36878732-chr5:36943861..36946469,3	K562	blood:

Variant related genes	Relation type
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10941319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743833	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744960	0.92[ASN][1000 genomes]
rs11745128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12153359	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12187383	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12188075	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12513653	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12516349	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12520272	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12520324	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12520562	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12521488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903365	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903373	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903403	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16903419	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16903427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903429	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16903442	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903456	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16903466	0.81[ASN][1000 genomes]
rs16903469	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16903477	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2365495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2365838	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776588	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849756	0.85[AMR][1000 genomes]
rs56680779	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56999464	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57686895	0.92[ASN][1000 genomes]
rs60633925	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60643425	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60730034	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61638663	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62654863	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16903413	RANBP3L	cis	cerebellum	SCAN
rs16903413	C5orf42	cis	cerebellum	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36919800-36953000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:36919800-36961600	Weak transcription	K562	blood
3	chr5:36920400-36951400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:36924800-36955200	Weak transcription	Dnd41	blood
5	chr5:36927600-36961600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:36929600-36947400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:36933200-36962000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:36933400-36949600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:36935200-36947200	Weak transcription	Primary T cells from cord blood	blood
10	chr5:36936000-36951600	Weak transcription	Primary B cells from cord blood	blood
11	chr5:36936800-36951000	Weak transcription	Right Ventricle	heart
12	chr5:36938000-36949200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr5:36938200-36945800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:36938200-36948200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:36938400-36946200	Weak transcription	Left Ventricle	heart
16	chr5:36939000-36945600	Weak transcription	Liver	Liver
17	chr5:36939200-36950800	Weak transcription	Ovary	ovary
18	chr5:36939400-36950800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr5:36939600-36950800	Weak transcription	Adipose Nuclei	Adipose
20	chr5:36939600-36954200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:36939600-36955400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr5:36940200-36946200	Weak transcription	Osteobl	bone
23	chr5:36940200-36950800	Weak transcription	Hela-S3	cervix
24	chr5:36940200-36955600	Weak transcription	Fetal Thymus	thymus
25	chr5:36940400-36950600	Weak transcription	HepG2	liver
26	chr5:36940600-36948400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:36940600-36949400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:36940600-36956000	Weak transcription	Fetal Intestine Small	intestine
29	chr5:36940600-36985400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr5:36940800-36945600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr5:36940800-36948200	Weak transcription	HSMM	muscle
32	chr5:36940800-36950400	Weak transcription	Fetal Intestine Large	intestine
33	chr5:36940800-36956600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr5:36941000-36946000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr5:36941200-36946000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:36941200-36947000	Weak transcription	A549	lung
37	chr5:36941200-36947600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr5:36941200-36950600	Weak transcription	GM12878-XiMat	blood
39	chr5:36941800-36946800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr5:36943600-36947400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:36944200-36950800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr5:36944200-36957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr5:36944400-36945600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr5:36944400-36945600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:36944400-36946200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr5:36944400-36946200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr5:36944400-36946200	Weak transcription	NHDF-Ad	bronchial
48	chr5:36944400-36950400	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:36944400-36955200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr5:36944600-36945600	Weak transcription	Colon Smooth Muscle	Colon

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