Variant report

Variant	rs223504
Chromosome Location	chr4:103635183-103635184
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs13112128	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]
rs170563	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs170564	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs223505	0.87[CEU][hapmap]
rs223508	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap]
rs223510	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap]
rs223512	0.96[CEU][hapmap]
rs227280	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs227283	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs227284	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs227285	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]
rs227369	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs227370	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs227372	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs393223	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs223504	MANBA	cis	lymphoblastoid	seeQTL
rs223504	CISD2	cis	cerebellum	SCAN
rs223504	MANBA	cis	cerebellum	SCAN
rs223504	ADH7	cis	cerebellum	SCAN
rs223504	KRT8P46	cis	lung	GTEx
rs223504	MANBA	cis	multi-tissue	Pritchard

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103547000-103658200	Weak transcription	Small Intestine	intestine
2	chr4:103553000-103651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:103553400-103651400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:103556200-103650400	Weak transcription	Pancreas	Pancrea
5	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:103580000-103644000	Weak transcription	Aorta	Aorta
8	chr4:103580400-103640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
10	chr4:103586000-103640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:103596200-103640600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr4:103608800-103644600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr4:103609200-103644000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr4:103609600-103640200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
16	chr4:103610000-103640600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr4:103611800-103635200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr4:103611800-103638800	Weak transcription	Liver	Liver
19	chr4:103612000-103644000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr4:103617000-103640200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:103618400-103655800	Weak transcription	HSMM	muscle
22	chr4:103622600-103643000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:103626800-103638600	Weak transcription	Ovary	ovary
24	chr4:103627000-103644200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:103627000-103650000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:103627200-103636000	Weak transcription	Left Ventricle	heart
27	chr4:103627200-103638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:103627400-103639200	Weak transcription	Fetal Intestine Small	intestine
29	chr4:103627400-103649800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:103627400-103650200	Weak transcription	Fetal Stomach	stomach
31	chr4:103627400-103650200	Weak transcription	Gastric	stomach
32	chr4:103627400-103650200	Weak transcription	Thymus	Thymus
33	chr4:103627400-103651000	Weak transcription	Right Ventricle	heart
34	chr4:103627400-103655400	Weak transcription	Lung	lung
35	chr4:103627600-103648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:103627600-103652400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr4:103628600-103640800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr4:103628800-103640800	Weak transcription	Dnd41	blood
39	chr4:103629000-103638800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr4:103629000-103639200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:103629800-103640600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:103629800-103644800	Weak transcription	Brain Substantia Nigra	brain
43	chr4:103630000-103644000	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr4:103630400-103655800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr4:103631000-103639200	Weak transcription	Fetal Thymus	thymus
46	chr4:103631200-103636600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr4:103631400-103640400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr4:103632000-103637200	Strong transcription	Primary B cells from cord blood	blood
49	chr4:103632000-103642000	Weak transcription	Brain Germinal Matrix	brain
50	chr4:103632400-103640800	Weak transcription	K562	blood

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