Variant report

Variant	rs2320339
Chromosome Location	chr2:95950045-95950046
allele	A/C
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	chr2:95949925-95950105	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:95944508..95946216-chr2:95948428..95950086,2	MCF-7	breast:

Variant related genes	Relation type
PROM2	TF binding region
ENSG00000155066	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10195614	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1104775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164122	0.91[EUR][1000 genomes]
rs11897976	0.89[EUR][1000 genomes]
rs12992066	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1559483	0.91[EUR][1000 genomes]
rs17119148	0.88[EUR][1000 genomes]
rs1862897	0.90[EUR][1000 genomes]
rs1875402	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1966272	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2001254	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2010533	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2042477	0.90[EUR][1000 genomes]
rs2098768	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2113417	0.89[EUR][1000 genomes]
rs2320621	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2320624	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3105102	0.83[EUR][1000 genomes]
rs3105104	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3105105	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112221	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112223	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112225	0.82[EUR][1000 genomes]
rs3112228	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3112229	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3112230	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3112231	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3112995	0.86[EUR][1000 genomes]
rs3112996	0.86[EUR][1000 genomes]
rs3112997	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3112999	0.83[EUR][1000 genomes]
rs3113000	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3113001	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3755519	0.90[EUR][1000 genomes]
rs3755520	0.91[EUR][1000 genomes]
rs3755521	0.91[EUR][1000 genomes]
rs3755523	0.91[EUR][1000 genomes]
rs3755525	0.93[EUR][1000 genomes]
rs3772031	0.90[EUR][1000 genomes]
rs3772032	0.90[EUR][1000 genomes]
rs3772033	0.90[EUR][1000 genomes]
rs3772034	0.85[EUR][1000 genomes]
rs3772037	0.90[EUR][1000 genomes]
rs3772041	0.91[EUR][1000 genomes]
rs3772042	0.91[EUR][1000 genomes]
rs3772043	0.93[EUR][1000 genomes]
rs3772044	0.96[EUR][1000 genomes]
rs3821341	0.87[EUR][1000 genomes]
rs4283455	0.90[EUR][1000 genomes]
rs4854247	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4854249	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6577012	0.91[EUR][1000 genomes]
rs6577013	0.91[EUR][1000 genomes]
rs6715813	0.91[EUR][1000 genomes]
rs6719098	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6725821	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6741001	0.90[EUR][1000 genomes]
rs6750542	0.90[EUR][1000 genomes]
rs7574862	0.91[EUR][1000 genomes]
rs7580685	0.91[EUR][1000 genomes]
rs7585914	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7586229	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7594144	0.91[EUR][1000 genomes]
rs7602807	0.89[EUR][1000 genomes]
rs870393	0.89[EUR][1000 genomes]
rs889851	0.91[EUR][1000 genomes]
rs889852	0.91[EUR][1000 genomes]
rs889853	0.91[EUR][1000 genomes]
rs918811	0.89[EUR][1000 genomes]
rs9678800	0.90[EUR][1000 genomes]
rs9989786	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817258	chr2:95618109-96340788	Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1008945	chr2:95745367-96062107	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv817299	chr2:95799814-96159275	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1007627	chr2:95878031-95973743	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv535822	chr2:95878031-95973743	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv998370	chr2:95897299-96074071	Flanking Active TSS Active TSS Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv535823	chr2:95897299-96074071	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv998014	chr2:95913278-96296630	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv528011	chr2:95931218-96057011	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1003196	chr2:95935031-95988314	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1010831	chr2:95935648-96074213	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv535824	chr2:95935648-96074213	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv482871	chr2:95936531-96036880	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv1010345	chr2:95939355-95988314	Genic enhancers Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv999838	chr2:95945923-96003473	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:95925600-95953800	Weak transcription	Right Atrium	heart
2	chr2:95926800-95953600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:95930000-95956200	Weak transcription	Fetal Brain Female	brain
4	chr2:95931400-95961000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:95931400-95961600	Weak transcription	Brain Substantia Nigra	brain
6	chr2:95932400-95961600	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:95941800-95954600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:95943000-95951400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:95943400-95952600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:95943600-95952600	Weak transcription	Lung	lung
11	chr2:95943600-95956200	Weak transcription	Right Ventricle	heart
12	chr2:95943800-95950800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:95944600-95955000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:95944800-95953600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:95944800-95955000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:95945800-95956400	Weak transcription	Ovary	ovary
17	chr2:95945800-95958200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:95946800-95956000	Weak transcription	Stomach Mucosa	stomach
19	chr2:95946800-95960000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:95947800-95951200	Strong transcription	Pancreas	Pancrea
21	chr2:95947800-95960800	Weak transcription	Brain Angular Gyrus	brain
22	chr2:95948400-95953800	Weak transcription	Brain Germinal Matrix	brain
23	chr2:95948400-95955800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr2:95948600-95952000	Weak transcription	Placenta	Placenta
25	chr2:95948600-95953400	Weak transcription	NHEK	skin
26	chr2:95948600-95957600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:95948800-95952600	Weak transcription	Fetal Stomach	stomach
28	chr2:95948800-95953400	Strong transcription	Esophagus	oesophagus
29	chr2:95948800-95954000	Weak transcription	Spleen	Spleen
30	chr2:95949000-95952800	Weak transcription	HMEC	breast
31	chr2:95949000-95953800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr2:95949200-95952800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr2:95949200-95952800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:95949400-95952400	Weak transcription	Colonic Mucosa	Colon
35	chr2:95949400-95953200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:95949600-95950200	Weak transcription	Gastric	stomach
37	chr2:95949800-95957200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:95950000-95956000	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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