Variant report

Variant	rs3736394
Chromosome Location	chr5:75888788-75888789
allele	C/T
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	MAFK	chr5:75888506-75888962	IMR90	lung:	n/a	chr5:75888701-75888716
2	MAFF	chr5:75888531-75888894	K562	blood:	n/a	chr5:75888699-75888717
3	MAFK	chr5:75888538-75888879	Hela-S3	cervix:	n/a	chr5:75888701-75888716
4	MAFK	chr5:75888243-75888986	GM12878	blood:	n/a	chr5:75888701-75888716
5	MAFK	chr5:75888515-75888900	HepG2	liver:	n/a	chr5:75888701-75888716
6	MAFF	chr5:75888529-75888907	HepG2	liver:	n/a	chr5:75888699-75888717
7	MAFK	chr5:75888534-75888891	HepG2	liver:	n/a	chr5:75888701-75888716
8	STAT3	chr5:75888775-75888964	MCF10A-Er-Src	breast:	n/a	n/a
9	MAFK	chr5:75888521-75889013	H1-hESC	embryonic stem cell:	n/a	chr5:75888701-75888716
10	MAFK	chr5:75888529-75888897	K562	blood:	n/a	chr5:75888701-75888716

Variant related genes	Relation type
IQGAP2	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10462543	0.95[JPT][hapmap]
rs11948805	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12513400	0.82[JPT][hapmap]
rs12523647	0.82[JPT][hapmap]
rs1501788	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17680732	0.82[JPT][hapmap]
rs17680756	0.95[JPT][hapmap]
rs17680811	0.95[JPT][hapmap]
rs17748322	0.86[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2011213	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3756514	0.82[JPT][hapmap]
rs3776768	0.86[MEX][hapmap]
rs3797378	0.86[ASN][1000 genomes]
rs3797387	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3797388	0.82[CHB][hapmap]
rs3822529	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3912001	0.95[JPT][hapmap]
rs4397115	0.80[AFR][1000 genomes]
rs4704329	0.95[JPT][hapmap]
rs4704336	0.82[MEX][hapmap]
rs6883527	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs869733	0.95[JPT][hapmap]
rs873787	0.95[JPT][hapmap]
rs879017	0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv598681	chr5:75863987-75902533	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3736394	TMEM171	cis	parietal	SCAN
rs3736394	CRHBP	cis	parietal	SCAN
rs3736394	AGGF1	cis	cerebellum	SCAN
rs3736394	TNPO1	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75846800-75902600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:75851800-75892000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:75853200-75896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:75861200-75889600	Weak transcription	Fetal Stomach	stomach
5	chr5:75873600-75903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:75874000-75892400	Weak transcription	Spleen	Spleen
7	chr5:75877000-75902800	Weak transcription	Adipose Nuclei	Adipose
8	chr5:75877400-75902800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr5:75879000-75892400	Weak transcription	Pancreas	Pancrea
10	chr5:75879000-75913600	Weak transcription	Colonic Mucosa	Colon
11	chr5:75879000-75917600	Weak transcription	Fetal Thymus	thymus
12	chr5:75879000-75934000	Weak transcription	Small Intestine	intestine
13	chr5:75879200-75888800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:75879200-75900600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:75879200-75907400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:75879200-75919000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:75879400-75903400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:75880200-75933400	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:75880600-75892600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:75880800-75897600	Weak transcription	HepG2	liver
21	chr5:75882000-75901400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
23	chr5:75882800-75892600	Weak transcription	Gastric	stomach
24	chr5:75883400-75904200	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr5:75884000-75890000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:75884000-75903000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr5:75884000-75914600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:75884200-75902200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr5:75884400-75890000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr5:75884400-75919200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:75884400-75919400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:75885000-75890400	Strong transcription	Placenta	Placenta
33	chr5:75885000-75891200	Strong transcription	Primary B cells from cord blood	blood
34	chr5:75885000-75891200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr5:75885200-75890200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:75885200-75900800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:75885400-75889800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr5:75885400-75890000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr5:75885400-75890200	Strong transcription	Primary T cells from cord blood	blood
40	chr5:75885400-75890400	Strong transcription	Liver	Liver
41	chr5:75885400-75893600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:75885400-75905000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr5:75886000-75889800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:75886000-75893600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:75886200-75902800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:75886400-75898600	Weak transcription	GM12878-XiMat	blood
47	chr5:75886600-75889000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr5:75886800-75889600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:75887200-75893000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:75888000-75892800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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