Variant report

Variant	rs227375
Chromosome Location	chr4:103618023-103618024
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 8 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17033015	0.80[YRI][hapmap]
rs223358	1.00[YRI][hapmap]
rs223397	1.00[YRI][hapmap]
rs223497	0.84[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs223498	0.89[CEU][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs227368	0.89[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs227375	MANBA	cis	cerebellum	SCAN
rs227375	ADH7	cis	cerebellum	SCAN
rs227375	CISD2	cis	parietal	SCAN
rs227375	CISD2	cis	cerebellum	SCAN
rs227375	RILP	trans	lymphoblastoid	seeQTL
rs227375	CISD2	cis	Nerve Tibial	GTEx
rs227375	MANBA	cis	multi-tissue	Pritchard
rs227375	CISD2	Cis_1M	lymphoblastoid	RTeQTL
rs227375	KRT8P46	cis	lung	GTEx

Chromatin state (count:66 , 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	chr4:103557600-103626400	Weak transcription	Lung	lung
6	chr4:103571800-103633600	Weak transcription	HepG2	liver
7	chr4:103571800-103655800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:103572000-103640800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:103580000-103644000	Weak transcription	Aorta	Aorta
10	chr4:103580400-103640600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:103581200-103627000	Weak transcription	Gastric	stomach
12	chr4:103581800-103681000	Weak transcription	Spleen	Spleen
13	chr4:103586000-103640600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr4:103590000-103626200	Weak transcription	Ovary	ovary
15	chr4:103594400-103624200	Weak transcription	Fetal Intestine Small	intestine
16	chr4:103596200-103640600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr4:103602400-103624800	Weak transcription	Placenta	Placenta
18	chr4:103604200-103626400	Weak transcription	Right Ventricle	heart
19	chr4:103606000-103626600	Weak transcription	Left Ventricle	heart
20	chr4:103608800-103644600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:103609200-103618600	Weak transcription	Brain Substantia Nigra	brain
22	chr4:103609200-103619000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr4:103609200-103644000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr4:103609400-103626400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:103609600-103624200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr4:103609600-103628200	Weak transcription	Fetal Heart	heart
27	chr4:103609600-103633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr4:103609600-103640200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:103609600-103664800	Weak transcription	Esophagus	oesophagus
30	chr4:103610000-103618200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:103610000-103626800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:103610000-103640600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:103611200-103620600	Weak transcription	Brain Hippocampus Middle	brain
34	chr4:103611200-103634400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr4:103611800-103635200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:103611800-103638800	Weak transcription	Liver	Liver
37	chr4:103612000-103633800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr4:103612000-103633800	Weak transcription	Adipose Nuclei	Adipose
39	chr4:103612000-103644000	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr4:103614800-103634000	Weak transcription	Fetal Intestine Large	intestine
41	chr4:103616000-103618200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr4:103616000-103618200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr4:103616000-103618400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr4:103616600-103628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr4:103616800-103619200	Weak transcription	Primary T cells from cord blood	blood
46	chr4:103617000-103618200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr4:103617000-103618200	Enhancers	Fetal Muscle Leg	muscle
48	chr4:103617000-103623600	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr4:103617000-103626200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:103617000-103640200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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