Variant report

Variant	rs311569
Chromosome Location	chr2:86295296-86295297
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	TCF12	chr2:86295241-86295486	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:86294765-86295420	K562	blood:	n/a	n/a
3	TCF12	chr2:86295263-86295553	GM12878	blood:	n/a	n/a
4	BHLHE40	chr2:86295258-86295569	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:86295142-86295342	HepG2	liver:	n/a	n/a
6	MXI1	chr2:86295141-86295474	GM12878	blood:	n/a	n/a
7	USF2	chr2:86295166-86295490	GM12878	blood:	n/a	n/a
8	SPI1	chr2:86295292-86295493	GM12878	blood:	n/a	n/a
9	ELF1	chr2:86295252-86295658	GM12878	blood:	n/a	n/a
10	ELF1	chr2:86295184-86295619	GM12878	blood:	n/a	n/a
11	MAZ	chr2:86295281-86295500	GM12878	blood:	n/a	n/a
12	CHD2	chr2:86295202-86295427	GM12878	blood:	n/a	n/a
13	RUNX3	chr2:86295242-86295607	GM12878	blood:	n/a	n/a
14	POLR2A	chr2:86295193-86295536	Hela-S3	cervix:	n/a	n/a
15	CTCF	chr2:86295180-86295330	GM12873	blood:	n/a	n/a
16	BATF	chr2:86295257-86295497	GM12878	blood:	n/a	n/a
17	POLR2A	chr2:86295206-86295487	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86283452..86286024-chr2:86293941..86297049,3	MCF-7	breast:

Variant related genes	Relation type
POLR1A	TF binding region

Extended variants
information (count: 89 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10165327	0.81[AMR][1000 genomes]
rs10176454	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10179090	0.81[AMR][1000 genomes]
rs10183744	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10187547	0.89[ASN][1000 genomes]
rs1019592	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs1025104	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs10427394	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs1075622	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs11127012	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11679343	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11686963	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11694973	0.98[ASN][1000 genomes]
rs12053229	0.98[ASN][1000 genomes]
rs12714168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1424517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1424520	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs1559515	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs1559516	0.87[CEU][hapmap]
rs1559517	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1834163	0.98[ASN][1000 genomes]
rs1991106	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2018547	0.88[ASN][1000 genomes]
rs2241436	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs2278086	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288118	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[ASN][1000 genomes]
rs2288119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2288120	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs2288121	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs2367201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2367202	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs3088038	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs311562	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs311563	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311565	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311566	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311567	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.98[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs311571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311572	0.92[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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs311573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs311581	0.85[CEU][hapmap]
rs311587	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3731820	0.98[ASN][1000 genomes]
rs3770069	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs3815840	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4618054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832021	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832022	0.98[ASN][1000 genomes]
rs4832241	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4832242	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs4832244	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4832245	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs4832246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4832249	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs4832250	0.87[CEU][hapmap];0.83[MEX][hapmap]
rs4832251	0.98[ASN][1000 genomes]
rs4832255	0.82[MEX][hapmap]
rs59947468	0.92[ASN][1000 genomes]
rs60479377	0.92[ASN][1000 genomes]
rs60719866	0.92[ASN][1000 genomes]
rs61620607	0.99[ASN][1000 genomes]
rs6720327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6740228	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs6741577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6750581	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]
rs6759862	0.98[ASN][1000 genomes]
rs725046	0.98[ASN][1000 genomes]
rs7559420	1.00[ASN][1000 genomes]
rs7562837	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7598787	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs7606421	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
4	nsv1007474	chr2:86281967-86505453	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv997563	chr2:86281967-86506132	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv1008924	chr2:86282722-86499402	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv999956	chr2:86285944-86505453	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv1012768	chr2:86285944-86506132	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
9	nsv1003207	chr2:86286314-86496732	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv1000441	chr2:86286314-86508168	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv535808	chr2:86286314-86508168	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
12	nsv1004442	chr2:86286480-86506132	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv916616	chr2:86289130-86509326	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv458563	chr2:86292341-86507688	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
15	nsv582370	chr2:86292341-86507688	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv1009140	chr2:86294939-86506132	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs311569	POLR1A	cis	Esophagus Muscularis	GTEx
rs311569	POLR1A	cis	Thyroid	GTEx
rs311569	PTCD3	cis	parietal	SCAN
rs311569	POLR1A	cis	parietal	SCAN
rs311569	C2orf89	cis	cerebellum	SCAN
rs311569	POLR1A	cis	Artery Tibial	GTEx
rs311569	POLR1A	cis	cerebellum	SCAN
rs311569	POLR1A	cis	Nerve Tibial	GTEx
rs311569	C2orf23	cis	multi-tissue	Pritchard
rs311569	POLR1A	cis	Stomach	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:86266400-86295800	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:86282600-86299200	Weak transcription	Small Intestine	intestine
7	chr2:86282800-86295800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:86285800-86299400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:86286000-86302200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:86286000-86331000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:86286000-86331200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:86286200-86298400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:86286200-86298600	Strong transcription	Fetal Lung	lung
14	chr2:86286200-86310400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:86286200-86311200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:86287000-86298800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:86289800-86296000	Weak transcription	Stomach Mucosa	stomach
18	chr2:86289800-86307200	Strong transcription	HepG2	liver
19	chr2:86290200-86295600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:86290200-86299400	Strong transcription	Hela-S3	cervix
21	chr2:86290200-86310800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:86290600-86297600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:86290600-86306200	Strong transcription	Fetal Intestine Large	intestine
24	chr2:86290800-86298200	Strong transcription	Liver	Liver
25	chr2:86290800-86299400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr2:86290800-86310200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:86290800-86314600	Strong transcription	HMEC	breast
28	chr2:86290800-86318600	Strong transcription	K562	blood
29	chr2:86290800-86322600	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr2:86291000-86298400	Strong transcription	Primary B cells from cord blood	blood
31	chr2:86291000-86311200	Strong transcription	Fetal Brain Female	brain
32	chr2:86291400-86299200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:86291600-86297600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr2:86291600-86319000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr2:86291800-86298000	Weak transcription	Fetal Brain Male	brain
36	chr2:86291800-86298800	Strong transcription	HUVEC	blood vessel
37	chr2:86291800-86299400	Strong transcription	GM12878-XiMat	blood
38	chr2:86291800-86311400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:86291800-86318800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:86292000-86298600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:86292000-86298600	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:86292400-86296000	Weak transcription	Aorta	Aorta
43	chr2:86292600-86295600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:86292600-86295800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:86292600-86296000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:86292600-86296000	Weak transcription	Pancreas	Pancrea
47	chr2:86292600-86296000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr2:86292800-86331000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:86293000-86295400	Weak transcription	Lung	lung
50	chr2:86293000-86297400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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