Variant report

Variant	rs13112128
Chromosome Location	chr4:103609793-103609794
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103603495..103606778-chr4:103609035..103613209,7	K562	blood:
2	chr4:103603807..103606307-chr4:103609358..103612973,3	K562	blood:

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs170563	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap]
rs170564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs223391	0.80[JPT][hapmap]
rs223408	0.80[JPT][hapmap]
rs223495	0.93[JPT][hapmap]
rs223496	0.93[JPT][hapmap]
rs223499	0.93[JPT][hapmap]
rs223500	0.93[JPT][hapmap]
rs223501	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs223502	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs223504	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs223505	1.00[CEU][hapmap]
rs223508	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap]
rs223510	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs223512	0.92[CEU][hapmap]
rs227280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs227283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs227284	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs227285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs227369	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap]
rs227370	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs227372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs393223	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008110	chr4:103560583-103684526	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1013963	chr4:103606672-103645082	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13112128	MANBA	cis	lymphoblastoid	seeQTL
rs13112128	MANBA	cis	cerebellum	SCAN
rs13112128	CISD2	cis	Temporal Cortex	GTEx
rs13112128	KRT8P46	cis	lung	GTEx
rs13112128	ADH7	cis	cerebellum	SCAN
rs13112128	MANBA	cis	multi-tissue	Pritchard
rs13112128	MANBA	cis	Liver	GTEx
rs13112128	TBCK	cis	parietal	SCAN
rs13112128	CISD2	cis	cerebellum	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103542400-103617400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
3	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
6	chr4:103557600-103626400	Weak transcription	Lung	lung
7	chr4:103559600-103617200	Weak transcription	Fetal Stomach	stomach
8	chr4:103561000-103614600	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:103563400-103617600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:103570800-103618000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:103571800-103611800	Weak transcription	Brain Anterior Caudate	brain
12	chr4:103571800-103633600	Weak transcription	HepG2	liver
13	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr4:103572800-103612600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr4:103579400-103615000	Weak transcription	Psoas Muscle	Psoas
17	chr4:103580000-103644000	Weak transcription	Aorta	Aorta
18	chr4:103580400-103640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr4:103581200-103627000	Weak transcription	Gastric	stomach
20	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
21	chr4:103585600-103613800	Weak transcription	Fetal Intestine Large	intestine
22	chr4:103586000-103640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:103589000-103618000	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:103590000-103626200	Weak transcription	Ovary	ovary
25	chr4:103590200-103610800	Weak transcription	Liver	Liver
26	chr4:103590200-103616800	Weak transcription	Fetal Lung	lung
27	chr4:103594200-103614000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:103594400-103610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr4:103594400-103617400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:103594400-103624200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:103594600-103612200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:103595200-103609800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr4:103595200-103617400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:103595800-103613800	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr4:103596000-103609800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:103596000-103610800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:103596200-103612000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr4:103596200-103640600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr4:103602400-103624800	Weak transcription	Placenta	Placenta
40	chr4:103604000-103617600	Weak transcription	Fetal Brain Male	brain
41	chr4:103604200-103610600	Weak transcription	Fetal Thymus	thymus
42	chr4:103604200-103616000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:103604200-103616800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr4:103604200-103626400	Weak transcription	Right Ventricle	heart
45	chr4:103604400-103617800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr4:103605000-103609800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:103605600-103611600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:103605600-103613400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:103606000-103610000	Enhancers	HMEC	breast
50	chr4:103606000-103614600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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