Variant report

Variant	rs1862937
Chromosome Location	chr3:120400415-120400416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1105765	0.82[CHD][hapmap]
rs17140269	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140398	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141991	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2236991	0.81[ASN][1000 genomes]
rs2236992	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2236993	0.81[ASN][1000 genomes]
rs2251584	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298958	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2551557	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733817	0.81[ASN][1000 genomes]
rs2733825	0.81[ASN][1000 genomes]
rs2733827	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2733828	0.96[ASN][1000 genomes]
rs3755563	0.81[ASN][1000 genomes]
rs3819371	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819372	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4143446	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676814	0.82[CHD][hapmap]
rs4676815	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676816	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676821	0.81[ASN][1000 genomes]
rs61795572	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61795573	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1862937	GTF2E1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120346400-120402200	Weak transcription	Gastric	stomach
2	chr3:120396600-120401200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:120397400-120400800	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr3:120397600-120400600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:120397600-120401400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:120397600-120401600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:120397600-120402200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:120397600-120407200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:120397600-120421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:120397800-120401200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:120397800-120401400	Weak transcription	Small Intestine	intestine
12	chr3:120397800-120410600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:120397800-120410600	Weak transcription	Brain Angular Gyrus	brain
14	chr3:120397800-120412200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:120397800-120415800	Weak transcription	Ovary	ovary
16	chr3:120397800-120420600	Weak transcription	Primary B cells from cord blood	blood
17	chr3:120397800-120421800	Weak transcription	Aorta	Aorta
18	chr3:120397800-120424800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:120398000-120405200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:120398200-120401000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:120398200-120401000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:120398200-120401200	Active TSS	Liver	Liver
23	chr3:120398200-120405800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:120398200-120407000	Weak transcription	GM12878-XiMat	blood
25	chr3:120398200-120408000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr3:120398200-120408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr3:120398200-120408200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:120398200-120410400	Weak transcription	Brain Substantia Nigra	brain
29	chr3:120398200-120412200	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:120398200-120412200	Weak transcription	HMEC	breast
31	chr3:120398200-120415200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr3:120398200-120423200	Weak transcription	Psoas Muscle	Psoas
33	chr3:120398200-120427000	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:120398200-120427800	Weak transcription	Placenta	Placenta
35	chr3:120398200-120430200	Weak transcription	NHEK	skin
36	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:120398400-120405200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:120398400-120407000	Weak transcription	Osteobl	bone
39	chr3:120398400-120412200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:120398400-120412400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:120398600-120401200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr3:120398600-120402000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:120398600-120411800	Weak transcription	HUVEC	blood vessel
44	chr3:120398800-120400800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:120398800-120401400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:120398800-120401800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:120399000-120400800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:120399200-120401400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr3:120399200-120401600	Enhancers	H1 Cell Line	embryonic stem cell

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