Variant report

Variant	rs744514
Chromosome Location	chr2:55846512-55846513
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55846359-55846754	K562	blood:	n/a	n/a
2	POLR2A	chr2:55846286-55846564	K562	blood:	n/a	n/a
3	POLR2A	chr2:55843453-55846870	H1-hESC	embryonic stem cell:	n/a	n/a
4	WRNIP1	chr2:55844622-55846735	GM12878	blood:	n/a	n/a
5	HEY1	chr2:55846323-55846677	K562	blood:	n/a	n/a
6	POLR2A	chr2:55843518-55846720	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:55843358-55846635	GM12878	blood:	n/a	n/a
8	MAX	chr2:55843499-55846678	HepG2	liver:	n/a	n/a
9	POLR2A	chr2:55846428-55846737	HepG2	liver:	n/a	n/a
10	HCFC1	chr2:55842863-55846662	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:55843559-55846735	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:55843645-55846748	GM12878	blood:	n/a	n/a
13	CTCF	chr2:55846380-55846530	HCPEpiC	choroid plexus:	n/a	n/a
14	POLR2A	chr2:55843444-55846832	GM12878	blood:	n/a	n/a
15	CTCF	chr2:55846400-55846550	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55846036..55847829-chr2:55873560..55876152,3	K562	blood:
2	chr2:55643936..55648492-chr2:55843198..55848689,6	K562	blood:
3	chr2:55843805..55846748-chr2:55896170..55899222,4	MCF-7	breast:
4	chr2:55845275..55847536-chr2:55874365..55876152,2	K562	blood:
5	chr2:55273795..55276620-chr2:55843969..55846667,2	K562	blood:
6	chr2:55644452..55648722-chr2:55843350..55848689,7	K562	blood:
7	chr2:55844652..55846516-chr2:55872491..55875236,2	MCF-7	breast:
8	chr2:55508376..55510742-chr2:55843787..55846796,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC104-3	chr2:55845115-55846902	NONHSAT070800

No data

Variant related genes	Relation type
SMEK2	TF binding region
ENSG00000138035	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000162997	Chromatin interaction
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10184287	0.80[JPT][hapmap]
rs10195281	0.86[AFR][1000 genomes]
rs10200159	0.84[AFR][1000 genomes]
rs10203953	0.84[AFR][1000 genomes]
rs10221888	0.80[YRI][hapmap]
rs1037508	0.90[ASN][1000 genomes]
rs10427222	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1045910	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10496044	0.82[YRI][hapmap]
rs10496049	0.87[YRI][hapmap]
rs11890141	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11900763	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12463766	0.90[ASN][1000 genomes]
rs12616502	0.97[YRI][hapmap]
rs12619756	0.83[ASN][1000 genomes]
rs12989898	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13016772	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13028892	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[ASN][1000 genomes]
rs13382187	0.84[YRI][hapmap]
rs13383352	0.84[YRI][hapmap]
rs13403782	0.85[ASN][1000 genomes]
rs13407344	0.83[YRI][hapmap]
rs1373228	0.83[JPT][hapmap]
rs1563201	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs17047094	0.97[YRI][hapmap];0.80[AFR][1000 genomes]
rs17047119	0.87[YRI][hapmap]
rs1975486	0.91[JPT][hapmap]
rs2168097	0.82[ASN][1000 genomes]
rs2586946	0.89[ASN][1000 genomes]
rs2586948	0.87[ASN][1000 genomes]
rs2586949	0.87[JPT][hapmap]
rs2586965	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2627758	0.88[ASN][1000 genomes]
rs2627763	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2627778	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2627783	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748945	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs3748955	0.90[AFR][1000 genomes]
rs3816489	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4233962	0.90[ASN][1000 genomes]
rs4671248	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs4671250	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62165178	0.91[ASN][1000 genomes]
rs6545503	0.90[JPT][hapmap]
rs6545505	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs6545508	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs6545510	0.97[YRI][hapmap];0.85[AFR][1000 genomes]
rs6545513	0.82[YRI][hapmap]
rs6712314	0.86[AFR][1000 genomes]
rs6716100	0.83[JPT][hapmap];0.81[YRI][hapmap]
rs6717574	0.96[YRI][hapmap]
rs6731927	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs6736996	0.86[AFR][1000 genomes]
rs6739788	0.89[YRI][hapmap]
rs6745430	0.91[AFR][1000 genomes]
rs6745650	0.96[YRI][hapmap]
rs6760959	0.97[YRI][hapmap];0.85[AFR][1000 genomes]
rs730884	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs736345	0.96[YRI][hapmap];0.96[AFR][1000 genomes]
rs7558127	0.80[YRI][hapmap]
rs7571482	0.87[ASN][1000 genomes]
rs7574398	0.85[AFR][1000 genomes]
rs7574409	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7585484	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7594497	0.82[YRI][hapmap]
rs7605486	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs7605504	0.83[ASN][1000 genomes]
rs782574	0.83[JPT][hapmap]
rs782589	0.84[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs782591	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs782593	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs782597	0.82[ASN][1000 genomes]
rs782598	0.89[ASN][1000 genomes]
rs782603	0.80[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs782612	0.88[ASN][1000 genomes]
rs782648	0.84[ASN][1000 genomes]
rs782651	0.84[ASN][1000 genomes]
rs9309267	0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs9309268	0.85[AFR][1000 genomes]
rs9636439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers 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 target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs744514	SMEK2	Cis_1M	lymphoblastoid	RTeQTL
rs744514	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55842600-55846800	Active TSS	H1 Cell Line	embryonic stem cell
2	chr2:55842800-55846800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:55842800-55847800	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr2:55843000-55846600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:55843000-55846600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:55843000-55846800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr2:55843000-55846800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:55843000-55846800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55843600-55846600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55843600-55846600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr2:55843600-55846600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:55843800-55846800	Active TSS	Rectal Smooth Muscle	rectum
13	chr2:55844000-55846600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
14	chr2:55844400-55846800	Active TSS	Fetal Brain Female	brain
15	chr2:55845000-55846800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:55845000-55847400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:55845200-55846600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr2:55845200-55846800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr2:55845800-55846800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr2:55846000-55846600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:55846000-55846600	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr2:55846000-55846600	Flanking Active TSS	Primary hematopoietic stem cells	blood
23	chr2:55846000-55846600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:55846000-55846800	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr2:55846000-55846800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr2:55846000-55846800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:55846000-55846800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
28	chr2:55846000-55846800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:55846000-55846800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:55846000-55846800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr2:55846000-55846800	Flanking Active TSS	Liver	Liver
32	chr2:55846000-55846800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr2:55846000-55847600	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr2:55846200-55846600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr2:55846200-55846600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr2:55846200-55846600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr2:55846200-55846600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:55846200-55846600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:55846200-55846600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:55846200-55846600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr2:55846200-55846600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr2:55846200-55846600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr2:55846200-55846600	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr2:55846200-55846600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr2:55846200-55846600	Flanking Active TSS	Fetal Brain Male	brain
46	chr2:55846200-55846600	Flanking Active TSS	Fetal Lung	lung
47	chr2:55846200-55846600	Flanking Active TSS	Stomach Mucosa	stomach
48	chr2:55846200-55846600	Flanking Active TSS	A549	lung
49	chr2:55846200-55846600	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr2:55846200-55846600	Flanking Active TSS	HUVEC	blood vessel

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