Variant report

Variant	rs2141991
Chromosome Location	chr3:120396975-120396976
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:56735335..56738268-chr3:120396094..120398851,2	MCF-7	breast:
2	chr3:120396369..120399119-chr3:120400893..120402859,2	K562	blood:
3	chr3:120396266..120398930-chr3:120408649..120411497,2	MCF-7	breast:
4	chr3:120382758..120384279-chr3:120395797..120398301,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000113924	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1105765	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs17140269	0.96[ASN][1000 genomes]
rs17140398	0.96[ASN][1000 genomes]
rs1862937	0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs2236991	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2236992	0.95[ASN][1000 genomes]
rs2236993	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2251584	0.95[ASN][1000 genomes]
rs2298956	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2298958	0.95[ASN][1000 genomes]
rs2551557	0.96[ASN][1000 genomes]
rs2733806	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733817	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733825	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733827	0.96[ASN][1000 genomes]
rs2733828	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755563	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3819371	0.96[ASN][1000 genomes]
rs3819372	0.95[ASN][1000 genomes]
rs4143446	0.96[ASN][1000 genomes]
rs4676704	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4676814	1.00[CEU][hapmap];0.82[CHD][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4676815	0.96[ASN][1000 genomes]
rs4676816	0.96[ASN][1000 genomes]
rs4676821	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61795572	0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2141991	SLC12A8	cis	cerebellum	SCAN
rs2141991	FSTL1	cis	cerebellum	SCAN
rs2141991	POLQ	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120346400-120402200	Weak transcription	Gastric	stomach
2	chr3:120347400-120398000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:120389600-120398600	Weak transcription	Pancreas	Pancrea
4	chr3:120391800-120400000	Weak transcription	Colonic Mucosa	Colon
5	chr3:120392200-120397000	Weak transcription	Brain Anterior Caudate	brain
6	chr3:120393000-120397000	Weak transcription	Brain Germinal Matrix	brain
7	chr3:120393000-120397200	Weak transcription	Fetal Brain Female	brain
8	chr3:120393400-120397000	Weak transcription	Small Intestine	intestine
9	chr3:120393800-120397200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:120394200-120397000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:120394600-120397000	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr3:120395400-120399200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:120395600-120397000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:120395600-120397000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:120396400-120398000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr3:120396600-120397000	Enhancers	HUVEC	blood vessel
17	chr3:120396600-120397200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr3:120396600-120397400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr3:120396600-120397600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:120396600-120397600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:120396600-120398200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:120396600-120398200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:120396600-120398800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:120396600-120399600	Enhancers	Stomach Mucosa	stomach
25	chr3:120396600-120399800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr3:120396600-120399800	Enhancers	Fetal Intestine Small	intestine
27	chr3:120396600-120400000	Enhancers	Fetal Intestine Large	intestine
28	chr3:120396600-120401200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr3:120396800-120397000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:120396800-120397000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:120396800-120397000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:120396800-120397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:120396800-120397000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:120396800-120397000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr3:120396800-120397000	Enhancers	Aorta	Aorta
36	chr3:120396800-120397000	Enhancers	Brain Cingulate Gyrus	brain
37	chr3:120396800-120397000	Enhancers	Brain Substantia Nigra	brain
38	chr3:120396800-120397000	Enhancers	Duodenum Mucosa	Duodenum
39	chr3:120396800-120397000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:120396800-120397000	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr3:120396800-120397000	Enhancers	Rectal Mucosa Donor 29	rectum
42	chr3:120396800-120397200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:120396800-120397200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:120396800-120397200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:120396800-120397200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:120396800-120397200	Active TSS	Brain Hippocampus Middle	brain
47	chr3:120396800-120397200	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr3:120396800-120397200	Flanking Active TSS	A549	lung
49	chr3:120396800-120397200	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr3:120396800-120397600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

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