Variant report

Variant	rs3765065
Chromosome Location	chr2:173420254-173420255
allele	A/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	chr2:173420038-173421535	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr2:173420233-173420962	K562	blood:	n/a	n/a
3	MAZ	chr2:173420152-173421433	Hela-S3	cervix:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663
4	PAX5	chr2:173420094-173420596	GM12891	blood:	n/a	n/a
5	HEY1	chr2:173420044-173421582	K562	blood:	n/a	chr2:173420723-173420738 chr2:173420648-173420663
6	REST	chr2:173419980-173421051	HepG2	liver:	n/a	n/a
7	POLR2A	chr2:173419900-173421978	IMR90	lung:	n/a	n/a
8	MAZ	chr2:173420011-173421758	IMR90	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
9	POLR2A	chr2:173419978-173421476	SK-N-MC	brain:	n/a	n/a
10	TCF7L2	chr2:173420176-173421435	HCT-116	colon:	n/a	n/a
11	TBP	chr2:173420102-173420927	GM12878	blood:	n/a	n/a
12	TEAD4	chr2:173420101-173420584	HepG2	liver:	n/a	n/a
13	PAX5	chr2:173420162-173421485	GM12892	blood:	n/a	chr2:173420605-173420614
14	CTBP2	chr2:173420223-173421477	H1-hESC	embryonic stem cell:	n/a	n/a
15	REST	chr2:173420236-173420648	A549	lung:	n/a	n/a
16	POU2F2	chr2:173420149-173420626	GM12891	blood:	n/a	n/a
17	POLR2A	chr2:173420109-173422237	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:173420089-173421467	Hela-S3	cervix:	n/a	n/a
19	ARID3A	chr2:173419374-173420584	K562	blood:	n/a	n/a
20	SP1	chr2:173420003-173420978	A549	lung:	n/a	chr2:173420781-173420790 chr2:173420781-173420790 chr2:173420690-173420699 chr2:173420655-173420664 chr2:173420691-173420700 chr2:173420654-173420666 chr2:173420690-173420704 chr2:173420654-173420666 chr2:173420730-173420742 chr2:173420656-173420665 chr2:173420678-173420685 chr2:173420782-173420791 chr2:173420780-173420792
21	STAT3	chr2:173419819-173420396	GM12878	blood:	n/a	n/a
22	MBD4	chr2:173420034-173421039	HepG2	liver:	n/a	n/a
23	TCF7L2	chr2:173420154-173420815	Hela-S3	cervix:	n/a	n/a
24	TBP	chr2:173420040-173421702	K562	blood:	n/a	n/a
25	MAX	chr2:173420050-173421939	Hela-S3	cervix:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
26	MYC	chr2:173420175-173420424	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr2:173419917-173421649	GM18951	blood:	n/a	n/a
28	MXI1	chr2:173419823-173421871	GM12878	blood:	n/a	n/a
29	POLR2A	chr2:173420041-173421556	HUVEC	blood vessel:	n/a	n/a
30	TBL1XR1	chr2:173419327-173420899	K562	blood:	n/a	n/a
31	HDAC2	chr2:173420240-173420477	K562	blood:	n/a	n/a
32	MAX	chr2:173419949-173421893	A549	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
33	PAX5	chr2:173420025-173421095	GM12878	blood:	n/a	chr2:173420605-173420614
34	MAX	chr2:173420075-173421861	A549	lung:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
35	SIN3AK20	chr2:173420188-173420613	H1-hESC	embryonic stem cell:	n/a	n/a
36	NR3C1	chr2:173420188-173420657	A549	lung:	n/a	n/a
37	TAF1	chr2:173420008-173421519	HepG2	liver:	n/a	n/a
38	MYC	chr2:173420205-173421472	MCF-7	breast:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663
39	CEBPD	chr2:173420107-173421011	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:173420001-173421520	H1-neurons	neurons:	n/a	n/a
41	CREB1	chr2:173420046-173421519	GM12878	blood:	n/a	n/a
42	POLR2A	chr2:173420181-173421309	K562	blood:	n/a	n/a
43	MAX	chr2:173420091-173421807	NB4	blood:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597
44	HCFC1	chr2:173420066-173421658	K562	blood:	n/a	n/a
45	MAX	chr2:173420037-173421000	SK-N-SH	brain:	n/a	chr2:173420751-173420761 chr2:173420653-173420663
46	POLR2A	chr2:173420144-173421433	Gliobla	brain:	n/a	n/a
47	POLR2A	chr2:173420076-173421546	GM18505	blood:	n/a	n/a
48	FOSL2	chr2:173420074-173420969	HepG2	liver:	n/a	n/a
49	POLR2A	chr2:173420061-173421694	HepG2	liver:	n/a	n/a
50	MAX	chr2:173419988-173421946	ECC-1	luminal epithelium:	n/a	chr2:173421339-173421354 chr2:173420751-173420761 chr2:173421613-173421622 chr2:173421328-173421338 chr2:173421341-173421356 chr2:173420653-173420663 chr2:173421615-173421622 chr2:173421611-173421626 chr2:173421588-173421597

No.	Distal block	Cell Line	Cell type
1	chr2:173420093..173420623-chr5:34007672..34008398,2	Hela-S3	cervix:
2	chr2:173420176..173421056-chr6:26043358..26044247,2	Hela-S3	cervix:
3	chr2:172966170..172969056-chr2:173419829..173422762,2	MCF-7	breast:
4	chr2:173420097..173422198-chr2:173422510..173426199,4	K562	blood:
5	chr11:32851440..32852221-chr2:173420119..173420696,2	Hela-S3	cervix:
6	chr2:173418979..173421868-chr2:173434562..173438051,3	K562	blood:
7	chr2:173351396..173353492-chr2:173418976..173421854,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLX2-4	chr2:173420154-173420308	ENSG00000225205.1

Variant related genes	Relation type
PDK1	TF binding region
ENSG00000242110	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000152256	Chromatin interaction
ENSG00000135378	Chromatin interaction
ENSG00000199866	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000091409	Chromatin interaction
ENSG00000115844	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10048692	0.80[EUR][1000 genomes]
rs10048707	0.80[EUR][1000 genomes]
rs10048825	0.80[EUR][1000 genomes]
rs10181851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186869	0.82[EUR][1000 genomes]
rs10199472	0.82[EUR][1000 genomes]
rs10208151	0.82[EUR][1000 genomes]
rs1075638	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10930561	0.93[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs10930562	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930563	0.84[ASN][1000 genomes]
rs10930565	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133602	0.86[ASN][1000 genomes]
rs11887454	0.82[EUR][1000 genomes]
rs11890159	0.82[EUR][1000 genomes]
rs11897165	0.82[EUR][1000 genomes]
rs11897495	0.81[EUR][1000 genomes]
rs11901110	0.82[EUR][1000 genomes]
rs11902810	0.81[EUR][1000 genomes]
rs11904158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11904366	0.81[EUR][1000 genomes]
rs12465704	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12476204	0.87[ASN][1000 genomes]
rs12693007	0.80[EUR][1000 genomes]
rs12693008	0.83[ASN][1000 genomes]
rs12990751	0.81[EUR][1000 genomes]
rs13007707	0.82[EUR][1000 genomes]
rs13008835	0.82[EUR][1000 genomes]
rs13009291	0.80[EUR][1000 genomes]
rs13015260	0.87[ASN][1000 genomes]
rs13019331	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13024563	0.86[ASN][1000 genomes]
rs13032610	0.80[EUR][1000 genomes]
rs13385403	0.83[EUR][1000 genomes]
rs13392808	0.82[EUR][1000 genomes]
rs13401676	0.90[ASN][1000 genomes]
rs13401980	0.82[EUR][1000 genomes]
rs13417334	0.82[EUR][1000 genomes]
rs1530864	0.93[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs1530865	0.88[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs1531150	0.81[ASN][1000 genomes]
rs1574257	0.85[CEU][hapmap]
rs16860693	0.88[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs16860696	0.83[EUR][1000 genomes]
rs16860697	0.83[EUR][1000 genomes]
rs16860737	0.87[ASN][1000 genomes]
rs16860741	0.86[ASN][1000 genomes]
rs17702263	0.82[EUR][1000 genomes]
rs1868901	0.86[ASN][1000 genomes]
rs1869923	0.84[ASN][1000 genomes]
rs2290563	0.81[YRI][hapmap]
rs2290564	0.83[EUR][1000 genomes]
rs2599260	0.84[ASN][1000 genomes]
rs2599261	0.84[ASN][1000 genomes]
rs2599262	0.84[ASN][1000 genomes]
rs2599263	0.84[ASN][1000 genomes]
rs2599264	0.84[ASN][1000 genomes]
rs2599265	0.84[ASN][1000 genomes]
rs2599266	0.84[ASN][1000 genomes]
rs2606062	0.84[ASN][1000 genomes]
rs2606063	0.84[ASN][1000 genomes]
rs2606064	0.83[ASN][1000 genomes]
rs2606065	0.84[ASN][1000 genomes]
rs2606066	0.84[ASN][1000 genomes]
rs2606067	0.84[ASN][1000 genomes]
rs2606070	0.84[ASN][1000 genomes]
rs34051646	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34139806	0.80[EUR][1000 genomes]
rs34707897	0.82[EUR][1000 genomes]
rs34888332	0.82[EUR][1000 genomes]
rs35809888	0.82[EUR][1000 genomes]
rs35880823	0.82[EUR][1000 genomes]
rs35892983	0.84[ASN][1000 genomes]
rs36118221	0.82[EUR][1000 genomes]
rs3769321	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61505737	0.80[ASN][1000 genomes]
rs62167835	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62169270	0.82[EUR][1000 genomes]
rs6710129	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6723872	0.83[EUR][1000 genomes]
rs6733679	0.84[ASN][1000 genomes]
rs6738196	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6752257	0.83[EUR][1000 genomes]
rs6752386	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs70937083	0.80[ASN][1000 genomes]
rs70937084	0.80[ASN][1000 genomes]
rs7584769	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8179584	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs836590	0.84[ASN][1000 genomes]
rs836629	0.84[ASN][1000 genomes]
rs836630	0.84[ASN][1000 genomes]
rs836631	0.84[ASN][1000 genomes]
rs836634	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv3035	chr2:173419058-173463901	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173419000-173423400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:173419200-173421400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:173419200-173422400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr2:173419400-173420400	Flanking Active TSS	HMEC	breast
5	chr2:173419400-173420400	Flanking Active TSS	K562	blood
6	chr2:173419400-173421600	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:173419600-173420400	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr2:173419600-173420400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr2:173419600-173420400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr2:173419600-173420400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:173419600-173420400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:173419600-173421400	Active TSS	Brain Anterior Caudate	brain
13	chr2:173419600-173421400	Active TSS	Rectal Mucosa Donor 31	rectum
14	chr2:173419600-173421400	Active TSS	Rectal Smooth Muscle	rectum
15	chr2:173419600-173421600	Active TSS	Fetal Kidney	kidney
16	chr2:173419600-173421600	Active TSS	Pancreas	Pancrea
17	chr2:173419600-173422000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr2:173419800-173420400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr2:173419800-173420400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:173419800-173420400	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr2:173419800-173420400	Flanking Active TSS	HUVEC	blood vessel
22	chr2:173419800-173420600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr2:173419800-173420600	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr2:173419800-173420600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:173419800-173421200	Active TSS	Stomach Smooth Muscle	stomach
26	chr2:173419800-173421400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr2:173419800-173421400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:173419800-173421400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:173419800-173421400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:173419800-173421400	Active TSS	Brain Substantia Nigra	brain
31	chr2:173419800-173421600	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr2:173419800-173421600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:173419800-173421600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:173419800-173421600	Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr2:173419800-173421600	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr2:173419800-173421600	Active TSS	A549	lung
37	chr2:173419800-173421800	Active TSS	Right Ventricle	heart
38	chr2:173419800-173422000	Active TSS	Right Atrium	heart
39	chr2:173419800-173422600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr2:173419800-173423400	Active TSS	H9 Cell Line	embryonic stem cell
41	chr2:173420000-173420400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr2:173420000-173420400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:173420000-173420400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr2:173420000-173420400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr2:173420000-173420400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:173420000-173420400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
47	chr2:173420000-173420400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr2:173420000-173420400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:173420000-173420400	Flanking Active TSS	Liver	Liver
50	chr2:173420000-173420400	Flanking Active TSS	Brain Angular Gyrus	brain

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