Variant report

Variant	rs902696
Chromosome Location	chr2:113954879-113954880
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113952947-113955870	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:113954868-113955566	GM12892	blood:	n/a	n/a
3	POLR2A	chr2:113954234-113955523	GM12891	blood:	n/a	n/a
4	POLR2A	chr2:113954528-113955688	GM12892	blood:	n/a	n/a
5	POLR2A	chr2:113953481-113955515	GM12878	blood:	n/a	n/a
6	POLR2A	chr2:113954667-113954909	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:113954228-113955590	GM12892	blood:	n/a	n/a
8	POLR2A	chr2:113954466-113954943	HL-60	blood:	n/a	n/a
9	POLR2A	chr2:113954373-113955695	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:113954744-113954935	K562	blood:	n/a	n/a
11	POLR2A	chr2:113954790-113955204	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113954862..113956783-chr2:113998620..114001129,2	MCF-7	breast:
2	chr2:113952804..113954880-chr2:113996400..113999228,2	MCF-7	breast:
3	chr2:113949482..113951925-chr2:113952977..113955662,3	K562	blood:
4	chr2:113912322..113918193-chr2:113953978..113958305,10	MCF-7	breast:
5	chr2:113913769..113918338-chr2:113954843..113958220,11	MCF-7	breast:
6	chr2:113950663..113952350-chr2:113953925..113956890,2	K562	blood:
7	chr2:113941477..113944460-chr2:113951684..113956081,4	K562	blood:

No data

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000125637	Chromatin interaction
ENSG00000258395	Chromatin interaction
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10175462	0.81[ASN][1000 genomes]
rs10206269	0.81[ASN][1000 genomes]
rs1110839	0.87[ASW][hapmap];0.81[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11123170	0.90[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs11123172	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs12612729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12619508	0.84[EUR][1000 genomes]
rs12620738	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374161	0.81[ASW][hapmap]
rs1466018	0.87[ASW][hapmap]
rs2015769	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2019137	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2305133	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2863243	0.81[ASN][1000 genomes]
rs3748916	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3811059	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3828188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3828189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848318	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849169	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4849177	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4849179	0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4849183	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62160781	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6707386	0.81[ASN][1000 genomes]
rs6751201	0.89[JPT][hapmap]
rs6755040	0.81[ASN][1000 genomes]
rs6755639	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs731834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[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];0.98[ASN][1000 genomes]
rs7421852	0.81[ASN][1000 genomes]
rs7563094	0.81[ASN][1000 genomes]
rs7578633	0.81[ASN][1000 genomes]
rs7589901	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs874898	0.94[JPT][hapmap]
rs895412	0.87[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs902695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv874900	chr2:113948378-113967990	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs902696	PAX8	cis	lung	GTEx
rs902696	PAX8	cis	Esophagus Mucosa	GTEx
rs902696	AC016683.6	cis	Esophagus Muscularis	GTEx
rs902696	AC016683.6	cis	Esophagus Mucosa	GTEx
rs902696	PAX8	cis	multi-tissue	Pritchard
rs902696	PAX8	cis	parietal	SCAN
rs902696	PAX8	cis	Adipose Subcutaneous	GTEx
rs902696	AC016683.6	cis	Nerve Tibial	GTEx
rs902696	AC016683.6	cis	Adipose Subcutaneous	GTEx
rs902696	LOC654433	cis	cerebellum	SCAN
rs902696	AC016683.6	cis	Muscle Skeletal	GTEx
rs902696	LOC654433	cis	parietal	SCAN
rs902696	AC016683.6	cis	Artery Tibial	GTEx
rs902696	LOC654433	Cis_1M	lymphoblastoid	RTeQTL
rs902696	PAX8	cis	Esophagus Muscularis	GTEx
rs902696	AC016683.6	cis	lung	GTEx
rs902696	PSD4	cis	lymphoblastoid	seeQTL
rs902696	PAX8	cis	lymphoblastoid	seeQTL
rs902696	AC016683.6	cis	Whole Blood	GTEx

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113956000	Weak transcription	HMEC	breast
2	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:113939400-113956400	Weak transcription	Small Intestine	intestine
5	chr2:113939600-113955400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:113939600-113956200	Weak transcription	Fetal Lung	lung
7	chr2:113940000-113961000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:113942800-113956600	Strong transcription	Fetal Thymus	thymus
9	chr2:113942800-113961000	Strong transcription	Dnd41	blood
10	chr2:113943000-113956200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:113943600-113956200	Weak transcription	Adipose Nuclei	Adipose
12	chr2:113943800-113955200	Weak transcription	Stomach Mucosa	stomach
13	chr2:113943800-113956000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:113947400-113961000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:113947600-113955800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr2:113947800-113955200	Strong transcription	Thymus	Thymus
17	chr2:113947800-113956200	Strong transcription	GM12878-XiMat	blood
18	chr2:113947800-113959600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:113947800-113960600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:113948400-113955000	Strong transcription	Liver	Liver
21	chr2:113948600-113955400	Strong transcription	Spleen	Spleen
22	chr2:113948600-113955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:113948600-113961000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:113948800-113955800	Strong transcription	Primary B cells from cord blood	blood
25	chr2:113948800-113955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:113948800-113955800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:113949000-113955800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:113949000-113956000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:113949000-113956000	Strong transcription	Primary B cells from peripheral blood	blood
30	chr2:113949000-113961200	Strong transcription	Primary neutrophils fromperipheralblood	blood
31	chr2:113949800-113955800	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr2:113950000-113955400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr2:113950000-113961000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:113950200-113955800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr2:113950600-113955400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:113951000-113955400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:113951000-113956200	Weak transcription	Fetal Kidney	kidney
38	chr2:113951000-113956400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:113951400-113955800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:113951400-113955800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:113951400-113956200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:113952400-113955600	Strong transcription	Esophagus	oesophagus
43	chr2:113952400-113956000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:113952600-113957800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr2:113952800-113956200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:113953200-113955400	Strong transcription	Fetal Intestine Small	intestine
47	chr2:113953400-113955400	Strong transcription	Lung	lung
48	chr2:113953400-113955600	Strong transcription	Placenta	Placenta
49	chr2:113953400-113956000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr2:113953600-113955800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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