Variant report

Variant	rs16903419
Chromosome Location	chr5:36952083-36952084
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFF	chr5:36951813-36952094	K562	blood:	n/a	n/a
2	GABPA	chr5:36952073-36952250	K562	blood:	n/a	chr5:36952171-36952180
3	MAFF	chr5:36951849-36952085	HepG2	liver:	n/a	n/a
4	SPI1	chr5:36951669-36952243	GM12878	blood:	n/a	chr5:36951876-36951889
5	SPI1	chr5:36951866-36952131	GM12891	blood:	n/a	chr5:36951876-36951889
6	SPI1	chr5:36951851-36952159	GM12891	blood:	n/a	chr5:36951876-36951889
7	MAFK	chr5:36951836-36952093	IMR90	lung:	n/a	n/a
8	SPI1	chr5:36951877-36952172	GM12878	blood:	n/a	n/a
9	SPI1	chr5:36951938-36952125	K562	blood:	n/a	n/a
10	MAFK	chr5:36951805-36952091	HepG2	liver:	n/a	n/a
11	SPI1	chr5:36951777-36952243	HL-60	blood:	n/a	chr5:36951876-36951889
12	SPI1	chr5:36951929-36952110	GM12878	blood:	n/a	n/a
13	SPI1	chr5:36951786-36952215	HL-60	blood:	n/a	chr5:36951876-36951889

No.	Distal block	Cell Line	Cell type
1	chr5:36743855..36746677-chr5:36948839..36952257,4	MCF-7	breast:
2	chr5:36875672..36878039-chr5:36951739..36953901,2	MCF-7	breast:
3	chr5:36951924..36954172-chr5:36959176..36961699,2	K562	blood:
4	chr5:36945026..36947869-chr5:36950785..36953502,2	K562	blood:

Variant related genes	Relation type
NIPBL	TF binding region
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10941319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.88[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][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]
rs11744960	0.89[ASN][1000 genomes]
rs11745128	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12153359	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12187383	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[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];0.89[ASN][1000 genomes]
rs12516349	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12520272	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12520324	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12520562	0.85[AMR][1000 genomes];0.81[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];0.89[ASN][1000 genomes]
rs16903365	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16903373	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16903403	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16903413	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];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903429	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16903442	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16903456	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16903469	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16903477	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2365495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2365838	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776588	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3822471	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3849756	0.85[AMR][1000 genomes]
rs56680779	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56999464	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57686895	0.89[ASN][1000 genomes]
rs60633925	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60643425	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60730034	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61638663	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62654863	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
15	nsv1034694	chr5:36946454-36991605	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv1015172	chr5:36946454-36993280	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv1033778	chr5:36946454-36994811	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv1033928	chr5:36947293-37039857	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
19	nsv917880	chr5:36948778-37115342	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16903419	RANBP3L	cis	cerebellum	SCAN
rs16903419	C5orf42	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

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	chr5:36924800-36955200	Weak transcription	Dnd41	blood
4	chr5:36927600-36961600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:36933200-36962000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:36939600-36954200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:36939600-36955400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr5:36940200-36955600	Weak transcription	Fetal Thymus	thymus
9	chr5:36940600-36956000	Weak transcription	Fetal Intestine Small	intestine
10	chr5:36940600-36985400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr5:36940800-36956600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr5:36944200-36957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:36944400-36955200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:36944800-36955400	Weak transcription	Placenta	Placenta
15	chr5:36945800-36953600	Weak transcription	Fetal Heart	heart
16	chr5:36946000-36957000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:36946200-36965000	Weak transcription	Psoas Muscle	Psoas
18	chr5:36946400-36955400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr5:36946400-36978000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:36946600-36955200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:36946600-36957000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:36946600-36970000	Weak transcription	Left Ventricle	heart
23	chr5:36946600-36976000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:36947600-36955000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:36948400-36955000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:36948400-36985800	Weak transcription	Colonic Mucosa	Colon
27	chr5:36948600-36962000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr5:36948600-36996600	Weak transcription	HSMMtube	muscle
29	chr5:36948800-36961800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:36949200-36952200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr5:36949600-36952200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:36949600-37086800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr5:36950400-36955800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr5:36950600-36952200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr5:36950600-36952200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:36950800-36952200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr5:36950800-36955400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr5:36951000-36952200	Enhancers	Brain Germinal Matrix	brain
39	chr5:36951000-36956000	Weak transcription	Fetal Stomach	stomach
40	chr5:36951000-36957200	Weak transcription	Primary T cells from cord blood	blood
41	chr5:36951000-36975800	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:36951200-36953600	Weak transcription	GM12878-XiMat	blood
43	chr5:36951200-36955600	Weak transcription	Liver	Liver
44	chr5:36951200-36957000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr5:36951200-36957800	Weak transcription	Ovary	ovary
46	chr5:36951200-36962200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr5:36951200-36968000	Weak transcription	Aorta	Aorta
48	chr5:36951400-36952200	Enhancers	Monocytes-CD14+_RO01746	blood
49	chr5:36951400-36952200	Enhancers	NHEK	skin
50	chr5:36951400-36953200	Weak transcription	Brain Hippocampus Middle	brain

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