Variant report

Variant	rs3133169
Chromosome Location	chr4:107258702-107258703
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:107238261..107242846-chr4:107256432..107259782,4	K562	blood:
2	chr4:107258354..107261291-chr4:107264865..107267295,3	K562	blood:

Variant related genes	Relation type
ENSG00000145348	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10000428	0.83[EUR][1000 genomes]
rs10003024	0.83[EUR][1000 genomes]
rs10004611	0.83[EUR][1000 genomes]
rs10008428	0.83[EUR][1000 genomes]
rs10017969	0.83[EUR][1000 genomes]
rs10027207	0.83[EUR][1000 genomes]
rs10049933	0.83[EUR][1000 genomes]
rs11732791	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11931386	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12642691	0.87[EUR][1000 genomes]
rs12650692	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13101612	0.87[EUR][1000 genomes]
rs13113845	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13114479	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13121614	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13138528	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2691804	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2949625	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2949650	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3018066	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3018069	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3109953	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3109955	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3109958	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3109960	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3113249	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3113250	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3113252	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3133168	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4307042	0.83[EUR][1000 genomes]
rs4374692	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4382109	0.83[EUR][1000 genomes]
rs4569824	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4600995	0.83[EUR][1000 genomes]
rs6533242	0.85[EUR][1000 genomes]
rs6819081	0.87[EUR][1000 genomes]
rs6836198	0.81[EUR][1000 genomes]
rs7356287	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7668276	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7673101	0.83[EUR][1000 genomes]
rs7682646	0.85[EUR][1000 genomes]
rs7693333	0.81[EUR][1000 genomes]
rs7693448	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9996093	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830029	chr4:107203096-107353483	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3133169	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs3133169	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107238600-107259600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:107238600-107259600	Weak transcription	Pancreas	Pancrea
3	chr4:107238800-107259000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:107239000-107259200	Weak transcription	Fetal Brain Male	brain
5	chr4:107239200-107259400	Weak transcription	Psoas Muscle	Psoas
6	chr4:107242800-107259400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr4:107243400-107271400	Weak transcription	Right Ventricle	heart
8	chr4:107243800-107259600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:107245600-107259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr4:107245800-107259000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:107245800-107261800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr4:107245800-107262200	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr4:107245800-107263000	Strong transcription	Dnd41	blood
14	chr4:107246000-107262000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr4:107246200-107262000	Strong transcription	NH-A	brain
16	chr4:107246400-107259400	Strong transcription	Placenta	Placenta
17	chr4:107246800-107260200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:107246800-107260800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr4:107247000-107258800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:107247000-107259600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr4:107247000-107260600	Strong transcription	Adipose Nuclei	Adipose
22	chr4:107247000-107261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:107247000-107261800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr4:107247000-107262000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr4:107247000-107262200	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr4:107247000-107263000	Strong transcription	Fetal Intestine Large	intestine
27	chr4:107247000-107263600	Strong transcription	Fetal Thymus	thymus
28	chr4:107247000-107271400	Strong transcription	Primary B cells from peripheral blood	blood
29	chr4:107247200-107260400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:107247400-107260600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:107247400-107262600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:107247600-107258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:107247600-107262400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:107247600-107263600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:107247800-107260600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:107248000-107259800	Strong transcription	Colon Smooth Muscle	Colon
37	chr4:107248000-107262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr4:107248400-107258800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr4:107248600-107261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:107248800-107260800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:107249000-107260800	Strong transcription	Osteobl	bone
42	chr4:107251000-107259200	Weak transcription	HSMMtube	muscle
43	chr4:107251600-107260000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr4:107252200-107262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr4:107252400-107260800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr4:107253200-107258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:107253200-107268200	Weak transcription	NHEK	skin
48	chr4:107254200-107260600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:107254200-107260800	Strong transcription	Left Ventricle	heart
50	chr4:107254400-107259600	Weak transcription	NHLF	lung

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