Variant report

Variant	rs12522926
Chromosome Location	chr5:179214818-179214819
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179127269..179130217-chr5:179212553..179215180,2	K562	blood:
2	chr5:179210097..179212795-chr5:179213653..179217175,3	MCF-7	breast:
3	chr5:179192837..179195567-chr5:179212671..179216209,3	K562	blood:
4	chr5:179213701..179215933-chr5:179218776..179220680,2	K562	blood:
5	chr5:179211965..179215539-chr5:179247804..179250502,3	K562	blood:
6	chr5:179210375..179212924-chr5:179213806..179215338,2	K562	blood:
7	chr5:179192355..179194197-chr5:179212856..179215229,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161011	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1019443	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10447303	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10447304	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10516146	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10794700	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10903245	0.83[AMR][1000 genomes]
rs11744662	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs12374446	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes]
rs12374485	0.83[AMR][1000 genomes]
rs12652934	0.81[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13172893	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13174472	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13182141	0.85[CEU][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.92[YRI][hapmap]
rs13184690	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34329357	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34646062	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs34785307	0.81[AMR][1000 genomes]
rs3797774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56227602	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62404348	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62406180	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6601073	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7736300	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
4	nsv469579	chr5:179184831-179360191	Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
5	nsv883274	chr5:179186397-179310330	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv518964	chr5:179193598-179227286	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
7	nsv883275	chr5:179193598-179267783	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
8	nsv883276	chr5:179193598-179310330	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
9	nsv883277	chr5:179193598-179350387	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	182 gene(s)	inside rSNPs	diseases
10	nsv823361	chr5:179213324-179251243	Genic enhancers Flanking Active TSS Enhancers Weak transcription 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	173 gene(s)	inside rSNPs	diseases
11	nsv600659	chr5:179214251-179225594	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	147 gene(s)	inside rSNPs	diseases
12	nsv600660	chr5:179214251-179231248	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	149 gene(s)	inside rSNPs	diseases
13	nsv883278	chr5:179214818-179238794	Active TSS Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	154 gene(s)	inside rSNPs	diseases
14	nsv883279	chr5:179214818-179248774	Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12522926	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL
rs12522926	C5orf45	cis	cerebellum	SCAN
rs12522926	CANX	cis	parietal	SCAN
rs12522926	MAML1	cis	lymphoblastoid	seeQTL
rs12522926	CANX	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179202000-179221800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr5:179203400-179218200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:179203400-179221600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:179203600-179219600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:179203600-179220400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:179203600-179222000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:179204000-179221200	Weak transcription	Small Intestine	intestine
8	chr5:179205000-179218800	Weak transcription	Right Atrium	heart
9	chr5:179205200-179220600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr5:179205200-179221800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr5:179206000-179220200	Weak transcription	Ovary	ovary
12	chr5:179206400-179219200	Weak transcription	Gastric	stomach
13	chr5:179207000-179220200	Weak transcription	GM12878-XiMat	blood
14	chr5:179207200-179215200	Weak transcription	HSMMtube	muscle
15	chr5:179207200-179218600	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:179207200-179218800	Weak transcription	Adipose Nuclei	Adipose
17	chr5:179207200-179220600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:179207400-179215200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:179207400-179218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:179207400-179219400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr5:179207400-179221000	Weak transcription	Brain Substantia Nigra	brain
22	chr5:179207600-179218800	Weak transcription	Fetal Lung	lung
23	chr5:179207600-179219200	Weak transcription	Colonic Mucosa	Colon
24	chr5:179207600-179219400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:179207600-179219400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr5:179207600-179220000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:179207600-179220200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:179207600-179220200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr5:179207600-179220200	Weak transcription	Pancreas	Pancrea
30	chr5:179207600-179220600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:179207600-179220800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:179207600-179221200	Weak transcription	Fetal Intestine Large	intestine
33	chr5:179207600-179222200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:179207600-179222600	Weak transcription	Aorta	Aorta
35	chr5:179207800-179215200	Weak transcription	Liver	Liver
36	chr5:179207800-179216200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:179207800-179218200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr5:179207800-179219200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr5:179207800-179220200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr5:179207800-179220200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr5:179207800-179220400	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:179207800-179220400	Weak transcription	Brain Angular Gyrus	brain
43	chr5:179207800-179220400	Weak transcription	HSMM	muscle
44	chr5:179207800-179220600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:179207800-179222200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr5:179208000-179215000	Weak transcription	NH-A	brain
47	chr5:179208000-179219400	Weak transcription	Primary B cells from cord blood	blood
48	chr5:179208000-179220200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr5:179208000-179220200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr5:179208000-179220400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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