Variant report

Variant	rs223502
Chromosome Location	chr4:103640758-103640759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:103635927..103637891-chr4:103639365..103641236,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs13112128	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs170563	0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs170564	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs223495	1.00[ASW][hapmap];0.84[CEU][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap]
rs223496	0.93[JPT][hapmap]
rs223499	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs223500	0.80[CEU][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap]
rs223501	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs223504	0.93[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs223508	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs223510	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs227280	0.93[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap]
rs227283	0.88[ASW][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs227284	0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs227285	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs227369	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs227370	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs227372	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs393223	0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs223502	MANBA	cis	cerebellum	SCAN
rs223502	TBCK	cis	parietal	SCAN
rs223502	MANBA	cis	lymphoblastoid	seeQTL
rs223502	CENPE	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

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	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
9	chr4:103608800-103644600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:103609200-103644000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
12	chr4:103612000-103644000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr4:103618400-103655800	Weak transcription	HSMM	muscle
14	chr4:103622600-103643000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:103627000-103644200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:103627000-103650000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:103627400-103649800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:103627400-103650200	Weak transcription	Fetal Stomach	stomach
19	chr4:103627400-103650200	Weak transcription	Gastric	stomach
20	chr4:103627400-103650200	Weak transcription	Thymus	Thymus
21	chr4:103627400-103651000	Weak transcription	Right Ventricle	heart
22	chr4:103627400-103655400	Weak transcription	Lung	lung
23	chr4:103627600-103648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:103627600-103652400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr4:103628600-103640800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr4:103628800-103640800	Weak transcription	Dnd41	blood
27	chr4:103629800-103644800	Weak transcription	Brain Substantia Nigra	brain
28	chr4:103630000-103644000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr4:103630400-103655800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:103632000-103642000	Weak transcription	Brain Germinal Matrix	brain
31	chr4:103632400-103640800	Weak transcription	K562	blood
32	chr4:103632400-103647800	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr4:103632400-103666200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr4:103632400-103667600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:103632800-103645400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr4:103632800-103651000	Weak transcription	Fetal Brain Female	brain
37	chr4:103633000-103647000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:103634000-103642600	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr4:103634000-103647200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr4:103634000-103650200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:103634000-103650400	Weak transcription	Brain Angular Gyrus	brain
42	chr4:103634400-103640800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:103634400-103644000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr4:103634400-103655400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:103634600-103644000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr4:103634600-103644000	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:103634600-103650200	Weak transcription	Fetal Intestine Large	intestine
48	chr4:103634600-103653400	Weak transcription	Fetal Lung	lung
49	chr4:103634600-103655400	Weak transcription	NHDF-Ad	bronchial
50	chr4:103634600-103655600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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