Variant report

Variant	rs3109953
Chromosome Location	chr4:107261003-107261004
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	chr4:107258354..107261291-chr4:107264865..107267295,3	K562	blood:
2	chr4:107255973..107258008-chr4:107260833..107262354,2	K562	blood:

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10000428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10003024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10004611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10008428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10017969	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10018910	0.94[ASN][1000 genomes]
rs10027207	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10049933	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11732791	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11931386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12642691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12650692	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13101612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13114479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13121614	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13138528	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17272618	0.94[ASN][1000 genomes]
rs2691804	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28467469	0.94[ASN][1000 genomes]
rs28784652	0.92[ASN][1000 genomes]
rs28805707	0.94[ASN][1000 genomes]
rs2949625	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2949650	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3018066	0.82[CEU][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3018069	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3109955	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3109958	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3113249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113250	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113252	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3133168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3133169	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4307042	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4314353	0.94[ASN][1000 genomes]
rs4374692	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4382109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4508971	0.94[ASN][1000 genomes]
rs4569824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4600995	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6533242	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6819081	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6836198	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6844105	0.94[ASN][1000 genomes]
rs6849573	0.94[ASN][1000 genomes]
rs7356287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7667596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7668276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7673101	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7682646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7692652	0.86[ASN][1000 genomes]
rs7693333	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7693448	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][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
rs3109953	MGC16169	Cis_1M	lymphoblastoid	RTeQTL
rs3109953	SCYE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:107243400-107271400	Weak transcription	Right Ventricle	heart
2	chr4:107245800-107261800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr4:107245800-107262200	Strong transcription	Rectal Mucosa Donor 29	rectum
4	chr4:107245800-107263000	Strong transcription	Dnd41	blood
5	chr4:107246000-107262000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:107246200-107262000	Strong transcription	NH-A	brain
7	chr4:107247000-107261200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:107247000-107261800	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr4:107247000-107262000	Strong transcription	Duodenum Mucosa	Duodenum
10	chr4:107247000-107262200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr4:107247000-107263000	Strong transcription	Fetal Intestine Large	intestine
12	chr4:107247000-107263600	Strong transcription	Fetal Thymus	thymus
13	chr4:107247000-107271400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr4:107247400-107262600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:107247600-107262400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr4:107247600-107263600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr4:107248000-107262000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr4:107248600-107261800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:107252200-107262400	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr4:107253200-107268200	Weak transcription	NHEK	skin
21	chr4:107255800-107262600	Strong transcription	Liver	Liver
22	chr4:107255800-107266800	Weak transcription	Stomach Mucosa	stomach
23	chr4:107256200-107266200	Weak transcription	HMEC	breast
24	chr4:107257200-107261800	Strong transcription	Ovary	ovary
25	chr4:107257600-107261200	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr4:107257600-107261800	Strong transcription	Brain Hippocampus Middle	brain
27	chr4:107257600-107262200	Strong transcription	Fetal Lung	lung
28	chr4:107257600-107262200	ZNF genes & repeats	GM12878-XiMat	blood
29	chr4:107257800-107262200	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr4:107257800-107262400	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr4:107258000-107262200	Strong transcription	Brain Anterior Caudate	brain
32	chr4:107258400-107261800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr4:107258400-107263000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:107258400-107263400	Weak transcription	Hela-S3	cervix
35	chr4:107258600-107262200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
36	chr4:107258600-107281400	Weak transcription	Fetal Heart	heart
37	chr4:107259000-107267600	Weak transcription	K562	blood
38	chr4:107259200-107262800	Strong transcription	Primary T cells from cord blood	blood
39	chr4:107259200-107265600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr4:107259400-107262400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr4:107259600-107261600	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr4:107259600-107261600	Weak transcription	Fetal Kidney	kidney
43	chr4:107259600-107270600	Weak transcription	Brain Substantia Nigra	brain
44	chr4:107259800-107262000	Strong transcription	HSMMtube	muscle
45	chr4:107259800-107263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr4:107259800-107263200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:107259800-107266600	Strong transcription	Primary B cells from cord blood	blood
48	chr4:107259800-107272400	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:107260000-107261200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr4:107260000-107261400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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