Variant report

Variant	rs41322849
Chromosome Location	chr2:64368260-64368261
allele	A/G
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	FOXA1	chr2:64367895-64368387	HepG2	liver:	n/a	chr2:64367934-64367946 chr2:64367930-64367942
2	CHD1	chr2:64366448-64368425	GM12878	blood:	n/a	n/a
3	ZNF384	chr2:64367720-64368288	K562	blood:	n/a	n/a
4	RFX5	chr2:64367819-64368265	K562	blood:	n/a	n/a
5	ZNF384	chr2:64367378-64368306	GM12878	blood:	n/a	n/a
6	EP300	chr2:64367992-64368263	K562	blood:	n/a	chr2:64368157-64368167

Variant related genes	Relation type
ENSG00000225889	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17028475	0.88[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028480	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028484	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028499	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028503	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028507	0.87[YRI][hapmap];0.84[AFR][1000 genomes]
rs17028509	0.87[YRI][hapmap];0.80[AFR][1000 genomes]
rs17028510	1.00[ASW][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17028513	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17039958	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41438647	0.98[AFR][1000 genomes]
rs60643329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893138	0.80[AFR][1000 genomes]
rs72893140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893152	1.00[AFR][1000 genomes]
rs72893157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893165	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893168	0.84[AFR][1000 genomes]
rs72893170	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893173	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72893180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64340400-64370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:64347400-64368800	Weak transcription	Spleen	Spleen
3	chr2:64355400-64368800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:64356200-64368600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:64356400-64368800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:64357200-64369600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:64359000-64368800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:64359000-64368800	Weak transcription	Right Ventricle	heart
9	chr2:64359400-64368600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:64360600-64368800	Weak transcription	Fetal Stomach	stomach
11	chr2:64361400-64368800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:64361800-64370000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:64362200-64368600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:64362400-64368800	Weak transcription	NH-A	brain
15	chr2:64362600-64368600	Enhancers	Primary T cells from cord blood	blood
16	chr2:64362600-64370000	Weak transcription	Ovary	ovary
17	chr2:64363200-64368800	Enhancers	Brain Substantia Nigra	brain
18	chr2:64363200-64368800	Enhancers	Colon Smooth Muscle	Colon
19	chr2:64364000-64370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:64364000-64370400	Weak transcription	Lung	lung
21	chr2:64364400-64368600	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr2:64364600-64369200	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:64365000-64368800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:64365400-64370800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:64365600-64368600	Enhancers	Brain Hippocampus Middle	brain
26	chr2:64365600-64368800	Weak transcription	Hela-S3	cervix
27	chr2:64365600-64370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:64365600-64370000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:64365600-64370000	Weak transcription	Placenta	Placenta
30	chr2:64365600-64370000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr2:64365800-64368600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:64365800-64368800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:64365800-64368800	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:64365800-64368800	Weak transcription	Small Intestine	intestine
35	chr2:64365800-64370200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:64365800-64370400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:64365800-64370400	Weak transcription	Esophagus	oesophagus
38	chr2:64366000-64368600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:64366000-64368600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:64366000-64368800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:64366000-64368800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:64366000-64369000	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr2:64366200-64368600	Weak transcription	Brain Angular Gyrus	brain
44	chr2:64366400-64368800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:64366400-64371800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr2:64366600-64368600	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr2:64366600-64368600	Enhancers	HMEC	breast
48	chr2:64366600-64368800	Enhancers	Rectal Smooth Muscle	rectum
49	chr2:64366600-64368800	Weak transcription	Thymus	Thymus
50	chr2:64366600-64370000	Weak transcription	Fetal Muscle Trunk	muscle

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