Variant report

Variant	rs6740127
Chromosome Location	chr2:37879796-37879797
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	chr2:37879540-37880005	GM12878	blood:	n/a	n/a
2	MTA3	chr2:37879311-37879841	GM12878	blood:	n/a	n/a
3	MAX	chr2:37879277-37879801	SK-N-SH	brain:	n/a	chr2:37879410-37879419
4	POLR2A	chr2:37879268-37879857	U87	brain:	n/a	n/a
5	POLR2A	chr2:37879291-37883487	GM12878	blood:	n/a	n/a
6	RELA	chr2:37879301-37879849	GM19099	blood:	n/a	n/a
7	RUNX3	chr2:37879253-37879903	GM12878	blood:	n/a	n/a
8	ELF1	chr2:37879255-37879840	SK-N-SH	brain:	n/a	chr2:37879526-37879535
9	BCL3	chr2:37879247-37879817	GM12878	blood:	n/a	chr2:37879419-37879428 chr2:37879526-37879535
10	POLR2A	chr2:37879230-37880580	HUVEC	blood vessel:	n/a	n/a
11	ZNF384	chr2:37879186-37880225	GM12878	blood:	n/a	n/a
12	PBX3	chr2:37879265-37879814	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr2:37879290-37879815	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr2:37879233-37880692	GM12892	blood:	n/a	n/a
15	POLR2A	chr2:37879344-37879832	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:37879266-37879870	GM12892	blood:	n/a	n/a
17	EBF1	chr2:37879291-37879919	GM12878	blood:	n/a	n/a
18	POLR2A	chr2:37879388-37884543	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:37879224-37884008	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:37879231-37879956	GM12891	blood:	n/a	n/a
21	MAX	chr2:37879296-37879796	SK-N-SH	brain:	n/a	chr2:37879410-37879419
22	TCF12	chr2:37879236-37880511	SK-N-SH	brain:	n/a	chr2:37879356-37879363
23	NFIC	chr2:37879258-37879946	SK-N-SH	brain:	n/a	n/a
24	NFIC	chr2:37879191-37879894	GM12878	blood:	n/a	n/a
25	MTA3	chr2:37879236-37883309	GM12878	blood:	n/a	n/a
26	POLR2A	chr2:37879295-37879995	GM12891	blood:	n/a	n/a
27	POLR2A	chr2:37879194-37884112	U87	brain:	n/a	n/a
28	NFIC	chr2:37879238-37881602	GM12878	blood:	n/a	n/a
29	GATA3	chr2:37879259-37880499	SK-N-SH	brain:	n/a	chr2:37879712-37879722 chr2:37879469-37879479 chr2:37879409-37879418
30	POLR2A	chr2:37879274-37879868	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr2:37879332-37884604	GM12878	blood:	n/a	n/a
32	POLR2A	chr2:37879214-37880682	SK-N-SH	brain:	n/a	n/a
33	POLR2A	chr2:37879578-37879830	A549	lung:	n/a	n/a
34	WRNIP1	chr2:37879452-37879890	GM12878	blood:	n/a	n/a
35	MXI1	chr2:37879238-37884627	SK-N-SH	brain:	n/a	chr2:37880975-37880984
36	NFATC1	chr2:37879243-37879891	GM12878	blood:	n/a	n/a
37	POLR2A	chr2:37879389-37880543	GM12892	blood:	n/a	n/a
38	POLR2A	chr2:37879323-37879918	GM12891	blood:	n/a	n/a
39	EBF1	chr2:37879344-37879884	GM12878	blood:	n/a	n/a
40	POLR2A	chr2:37879268-37879844	U87	brain:	n/a	n/a
41	TCF12	chr2:37879241-37879870	SK-N-SH	brain:	n/a	chr2:37879356-37879363
42	RUNX3	chr2:37879300-37879876	GM12878	blood:	n/a	n/a
43	GATA3	chr2:37879247-37880654	SK-N-SH	brain:	n/a	chr2:37879712-37879722 chr2:37879469-37879479 chr2:37879409-37879418
44	POLR2A	chr2:37879356-37882971	GM18505	blood:	n/a	n/a
45	POLR2A	chr2:37879143-37884106	U87	brain:	n/a	n/a
46	POLR2A	chr2:37879335-37882967	GM12892	blood:	n/a	n/a
47	POLR2A	chr2:37879348-37888136	GM12891	blood:	n/a	n/a
48	STAT3	chr2:37879192-37879863	MCF10A-Er-Src	breast:	n/a	chr2:37879478-37879489
49	POLR2A	chr2:37879248-37880043	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:37878873..37880892-chr2:37884421..37886893,2	K562	blood:
2	chr2:37877539..37880523-chr2:37887000..37889009,2	K562	blood:
3	chr2:37869759..37872018-chr2:37878989..37880854,2	MCF-7	breast:

Variant related genes	Relation type
CDC42EP3	TF binding region

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1013291	0.84[ASN][1000 genomes]
rs1013292	0.82[ASN][1000 genomes]
rs10694	0.88[ASN][1000 genomes]
rs11124594	0.86[ASN][1000 genomes]
rs11124595	0.86[ASN][1000 genomes]
rs11883958	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12622958	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13387842	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13392288	0.84[ASN][1000 genomes]
rs13406302	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13417957	0.81[ASN][1000 genomes]
rs1468663	0.84[ASN][1000 genomes]
rs1468664	0.83[ASN][1000 genomes]
rs17021174	0.86[ASN][1000 genomes]
rs2041508	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2072419	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2079998	0.84[ASN][1000 genomes]
rs2098198	0.84[ASN][1000 genomes]
rs2109821	0.84[ASN][1000 genomes]
rs2109822	0.84[ASN][1000 genomes]
rs2159726	0.84[ASN][1000 genomes]
rs2191841	0.84[ASN][1000 genomes]
rs2373290	0.84[ASN][1000 genomes]
rs3731852	0.88[ASN][1000 genomes]
rs3731854	0.87[ASN][1000 genomes]
rs4372883	0.84[ASN][1000 genomes]
rs4594425	0.84[ASN][1000 genomes]
rs4670210	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4670211	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4670748	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56809883	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6544095	0.88[ASN][1000 genomes]
rs67084656	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6709067	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6709621	0.90[ASN][1000 genomes]
rs6711909	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6722589	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6752119	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6752220	0.94[ASN][1000 genomes]
rs6752762	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6759224	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7607934	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7735	0.88[ASN][1000 genomes]
rs9742	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
5	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
9	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
10	chr2:37873000-37881400	Enhancers	Right Atrium	heart
11	chr2:37873600-37880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:37873600-37881000	Weak transcription	Ovary	ovary
13	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:37874200-37881600	Genic enhancers	NHLF	lung
15	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
16	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
17	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
18	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr2:37874800-37880000	Genic enhancers	Lung	lung
20	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
21	chr2:37875200-37881800	Enhancers	Spleen	Spleen
22	chr2:37875200-37882200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:37875400-37881200	Enhancers	Primary B cells from peripheral blood	blood
24	chr2:37875400-37883400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:37875600-37881000	Weak transcription	Fetal Brain Female	brain
26	chr2:37875600-37881200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:37875800-37880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr2:37875800-37881000	Weak transcription	Brain Germinal Matrix	brain
29	chr2:37875800-37881600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr2:37875800-37882000	Enhancers	Right Ventricle	heart
31	chr2:37875800-37883800	Genic enhancers	NHDF-Ad	bronchial
32	chr2:37875800-37884400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:37875800-37891800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:37875800-37893600	Weak transcription	Fetal Intestine Large	intestine
35	chr2:37875800-37896400	Weak transcription	Fetal Intestine Small	intestine
36	chr2:37876000-37880200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:37876000-37880600	Weak transcription	Brain Angular Gyrus	brain
38	chr2:37876000-37881000	Weak transcription	Fetal Lung	lung
39	chr2:37876000-37881000	Genic enhancers	HSMM	muscle
40	chr2:37876000-37881200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:37876000-37882800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr2:37876200-37880000	Enhancers	Stomach Smooth Muscle	stomach
43	chr2:37876200-37880200	Enhancers	Primary B cells from cord blood	blood
44	chr2:37876200-37880400	Weak transcription	Aorta	Aorta
45	chr2:37876200-37880800	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr2:37876200-37881000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr2:37876200-37881000	Weak transcription	Thymus	Thymus
48	chr2:37876200-37881200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:37876200-37881400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:37876200-37882600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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