Variant report

Variant	rs11923513
Chromosome Location	chr3:134090793-134090794
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:134086773-134094473	Hela-S3	cervix:	n/a	n/a
2	TEAD4	chr3:134090369-134090794	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:134086772-134094312	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr3:134089522-134090875	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr3:134086769-134091751	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr3:134090169-134090812	HCT-116	colon:	n/a	n/a
7	POLR2A	chr3:134090064-134093861	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr3:134090674-134093906	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:134079921-134092871	ECC-1	luminal epithelium:	n/a	n/a
10	CHD1	chr3:134070900-134094634	IMR90	lung:	n/a	chr3:134093783-134093793 chr3:134092557-134092567 chr3:134083055-134083065
11	POLR2A	chr3:134089460-134093902	ProgFib	skin:	n/a	n/a
12	POLR2A	chr3:134088558-134094000	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:134071087-134094366	Hela-S3	cervix:	n/a	n/a
14	GATA2	chr3:134090398-134091631	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr3:134084882-134093800	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:134071303-134093679	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:134090521-134093751	HUVEC	blood vessel:	n/a	n/a
18	POLR2A	chr3:134090018-134093825	HUVEC	blood vessel:	n/a	n/a
19	GATA3	chr3:134090785-134091191	MCF-7	breast:	n/a	n/a
20	POLR2A	chr3:134090064-134091739	SK-N-SH	brain:	n/a	n/a
21	RAD21	chr3:134090072-134094108	IMR90	lung:	n/a	chr3:134093425-134093437 chr3:134091918-134091931 chr3:134093415-134093427
22	MAZ	chr3:134085077-134094456	IMR90	lung:	n/a	chr3:134092343-134092353 chr3:134093443-134093453 chr3:134087585-134087594
23	POLR2A	chr3:134074967-134094367	PANC-1	pancreas:	n/a	n/a
24	EP300	chr3:134088772-134091019	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr3:134080043-134092973	A549	lung:	n/a	n/a
26	POLR2A	chr3:134080609-134094580	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr3:134079902-134094732	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr3:134090657-134090870	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr3:134080444-134091779	PANC-1	pancreas:	n/a	n/a
30	POLR2A	chr3:134086786-134094411	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr3:134089814-134091771	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr3:134069355-134094620	IMR90	lung:	n/a	n/a
33	POLR2A	chr3:134083318-134094139	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:65587328..65588998-chr3:134088720..134091228,2	MCF-7	breast:
2	chr3:134089711..134094738-chr3:134202793..134208651,12	MCF-7	breast:
3	chr3:134024307..134037207-chr3:134080573..134100993,88	MCF-7	breast:

Variant related genes	Relation type
AMOTL2	TF binding region
ENSG00000240006	Chromatin interaction
ENSG00000199568	Chromatin interaction
ENSG00000129055	Chromatin interaction
ENSG00000182923	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10935116	1.00[CHB][hapmap]
rs11707704	1.00[ASN][1000 genomes]
rs11917363	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11919447	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11928672	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11928742	1.00[CHB][hapmap]
rs11928907	1.00[ASN][1000 genomes]
rs12487438	1.00[CHB][hapmap]
rs13069766	1.00[ASN][1000 genomes]
rs13071132	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13078237	0.84[AMR][1000 genomes]
rs13084853	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13090504	1.00[ASN][1000 genomes]
rs1498730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[ASN][1000 genomes]
rs17312996	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17313003	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991440	0.89[EUR][1000 genomes]
rs34006849	1.00[ASN][1000 genomes]
rs34524468	1.00[ASN][1000 genomes]
rs34549392	1.00[ASN][1000 genomes]
rs35098409	1.00[ASN][1000 genomes]
rs35471660	1.00[ASN][1000 genomes]
rs35527623	1.00[ASN][1000 genomes]
rs35558600	1.00[ASN][1000 genomes]
rs35878592	1.00[ASN][1000 genomes]
rs3846052	1.00[ASN][1000 genomes]
rs3913262	1.00[ASN][1000 genomes]
rs4339087	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs5002434	1.00[ASN][1000 genomes]
rs5002435	1.00[ASN][1000 genomes]
rs5002436	1.00[ASN][1000 genomes]
rs5002437	1.00[ASN][1000 genomes]
rs55682444	1.00[ASN][1000 genomes]
rs56019901	1.00[ASN][1000 genomes]
rs59458665	1.00[ASN][1000 genomes]
rs61145443	1.00[ASN][1000 genomes]
rs62271221	1.00[ASN][1000 genomes]
rs6439474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6439476	1.00[ASN][1000 genomes]
rs6768709	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6772791	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6776727	1.00[ASN][1000 genomes]
rs6784751	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6804439	1.00[ASN][1000 genomes]
rs6809909	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs71331755	1.00[ASN][1000 genomes]
rs72986454	1.00[ASN][1000 genomes]
rs73215399	1.00[ASN][1000 genomes]
rs7609766	1.00[ASN][1000 genomes]
rs7613323	1.00[ASN][1000 genomes]
rs7613440	1.00[ASN][1000 genomes]
rs7613450	1.00[ASN][1000 genomes]
rs7614069	1.00[ASN][1000 genomes]
rs7636249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7637889	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7638751	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7642519	1.00[ASN][1000 genomes]
rs7647682	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7647778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7651578	1.00[ASN][1000 genomes]
rs9826364	1.00[CHB][hapmap];1.00[CHD][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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers 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	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11923513	PRR23C	cis	cerebellum	SCAN
rs11923513	TMEM22	cis	parietal	SCAN
rs11923513	COPB2	cis	cerebellum	SCAN
rs11923513	CCRL1	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134072400-134091200	Genic enhancers	Spleen	Spleen
2	chr3:134073400-134091400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:134081600-134091000	Enhancers	Psoas Muscle	Psoas
4	chr3:134082000-134090800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:134082000-134090800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:134082000-134091000	Genic enhancers	Fetal Stomach	stomach
7	chr3:134082200-134092800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:134082400-134091400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:134083600-134090800	Genic enhancers	Fetal Intestine Large	intestine
10	chr3:134084000-134090800	Genic enhancers	Lung	lung
11	chr3:134084600-134090800	Genic enhancers	Aorta	Aorta
12	chr3:134085800-134090800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:134086000-134091000	Genic enhancers	HepG2	liver
14	chr3:134087200-134092600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:134087400-134091600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr3:134087600-134091200	Genic enhancers	Fetal Lung	lung
17	chr3:134087600-134091400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
18	chr3:134087600-134092400	Transcr. at gene 5' and 3'	A549	lung
19	chr3:134087800-134091600	Transcr. at gene 5' and 3'	HSMM	muscle
20	chr3:134087800-134091800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
21	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
22	chr3:134087800-134092600	Transcr. at gene 5' and 3'	Osteobl	bone
23	chr3:134088000-134090800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:134088000-134091000	Transcr. at gene 5' and 3'	NH-A	brain
25	chr3:134088000-134091400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:134088000-134091600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
27	chr3:134088200-134092600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr3:134088400-134091200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr3:134088400-134092200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:134088400-134092600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:134088600-134091400	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
32	chr3:134088600-134091600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
33	chr3:134088600-134092400	Transcr. at gene 5' and 3'	NHLF	lung
34	chr3:134088800-134091000	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr3:134088800-134091200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
36	chr3:134088800-134091200	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
37	chr3:134088800-134091600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr3:134089000-134091000	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:134089200-134092600	Transcr. at gene 5' and 3'	NHEK	skin
40	chr3:134089400-134090800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:134089400-134090800	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
42	chr3:134089400-134091000	Genic enhancers	H1 Cell Line	embryonic stem cell
43	chr3:134089400-134091000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:134089400-134091200	Transcr. at gene 5' and 3'	Brain Cingulate Gyrus	brain
45	chr3:134089400-134091400	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
46	chr3:134089400-134091600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
47	chr3:134089400-134091600	Transcr. at gene 5' and 3'	HMEC	breast
48	chr3:134089400-134092400	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
49	chr3:134089600-134091000	Enhancers	Fetal Brain Male	brain
50	chr3:134089600-134091200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain

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