Variant report

Variant	rs28437577
Chromosome Location	chr14:39640674-39640675
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:39638939-39640740	SK-N-MC	brain:	n/a	n/a
2	MBD4	chr14:39638508-39640680	HepG2	liver:	n/a	n/a
3	NFIC	chr14:39639967-39640730	HepG2	liver:	n/a	n/a
4	HEY1	chr14:39640003-39640720	HepG2	liver:	n/a	n/a
5	MYC	chr14:39638972-39640711	K562	blood:	n/a	n/a
6	POLR2A	chr14:39638293-39640766	PBDE	blood:	n/a	n/a
7	MAX	chr14:39640510-39640796	K562	blood:	n/a	n/a
8	POLR2A	chr14:39639989-39640785	HepG2	liver:	n/a	n/a
9	MAX	chr14:39640567-39640760	K562	blood:	n/a	n/a
10	HCFC1	chr14:39638711-39640710	Hela-S3	cervix:	n/a	n/a
11	E2F6	chr14:39640596-39640749	K562	blood:	n/a	n/a
12	POLR2A	chr14:39638667-39640876	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39627588..39630003-chr14:39640583..39643561,2	MCF-7	breast:
2	chr14:39576976..39580513-chr14:39638047..39641153,4	K562	blood:
3	chr14:39638891..39641141-chr14:39697742..39700523,2	MCF-7	breast:
4	chr14:39583285..39585580-chr14:39639274..39641168,2	K562	blood:
5	chr14:39639912..39642266-chr14:39694401..39697374,2	K562	blood:
6	chr14:39582622..39586619-chr14:39638047..39642701,6	MCF-7	breast:
7	chr14:39636108..39642775-chr14:39734196..39739360,12	MCF-7	breast:
8	chr14:39639668..39641561-chr14:39735977..39737875,2	K562	blood:
9	chr14:39572251..39574864-chr14:39637876..39641106,3	MCF-7	breast:
10	chr14:39638023..39641762-chr14:39900094..39905872,5	MCF-7	breast:
11	chr14:39570348..39574070-chr14:39637691..39640941,4	MCF-7	breast:

No data

Variant related genes	Relation type
TRAPPC6B	TF binding region
PNN	TF binding region
ENSG00000258941	Chromatin interaction
ENSG00000092208	Chromatin interaction
ENSG00000258591	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000150526	Chromatin interaction
ENSG00000165355	Chromatin interaction
ENSG00000258651	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1002193	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10129762	0.81[ASN][1000 genomes]
rs10131369	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10134166	0.84[ASN][1000 genomes]
rs10135561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10136637	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10140763	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10141924	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10142117	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10142350	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10145417	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10145476	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10146176	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10148712	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1050136	0.99[ASN][1000 genomes]
rs11622731	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11622968	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11624584	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11626002	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11628784	0.83[ASN][1000 genomes]
rs11849209	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11850579	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11851680	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587208	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13021	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13379129	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17092044	0.83[ASN][1000 genomes]
rs17092050	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17108948	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2273592	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28501673	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28583114	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28666016	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28701960	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28821293	0.83[ASN][1000 genomes]
rs45622837	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57326310	0.83[ASN][1000 genomes]
rs57482489	0.83[ASN][1000 genomes]
rs57555422	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58601678	0.83[ASN][1000 genomes]
rs59465524	0.83[ASN][1000 genomes]
rs7155307	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74048710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74048711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761805	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[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	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1813567	chr14:39632114-39642840	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39640000-39643400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:39640000-39643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:39640000-39643400	Weak transcription	Spleen	Spleen
4	chr14:39640000-39643600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr14:39640000-39643600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:39640000-39643600	Weak transcription	Left Ventricle	heart
7	chr14:39640000-39644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:39640200-39640800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr14:39640200-39640800	Enhancers	Primary B cells from cord blood	blood
10	chr14:39640200-39640800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr14:39640200-39640800	Flanking Active TSS	HepG2	liver
12	chr14:39640200-39643400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr14:39640400-39640800	Enhancers	H1 Cell Line	embryonic stem cell
14	chr14:39640400-39640800	Enhancers	Fetal Intestine Small	intestine
15	chr14:39640400-39640800	Enhancers	Fetal Muscle Trunk	muscle
16	chr14:39640400-39640800	Enhancers	Fetal Muscle Leg	muscle
17	chr14:39640400-39640800	Enhancers	Stomach Mucosa	stomach
18	chr14:39640400-39641000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr14:39640400-39643200	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr14:39640400-39643200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr14:39640400-39643200	Weak transcription	Colonic Mucosa	Colon
22	chr14:39640400-39643400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr14:39640400-39643400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr14:39640400-39643400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:39640400-39643400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:39640400-39643400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr14:39640400-39643400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr14:39640400-39643400	Weak transcription	Brain Germinal Matrix	brain
29	chr14:39640400-39643400	Weak transcription	Fetal Thymus	thymus
30	chr14:39640400-39643600	Weak transcription	Fetal Brain Female	brain
31	chr14:39640400-39643600	Weak transcription	Placenta	Placenta
32	chr14:39640600-39640800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr14:39640600-39640800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr14:39640600-39640800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:39640600-39640800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr14:39640600-39640800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr14:39640600-39640800	Enhancers	A549	lung
38	chr14:39640600-39640800	Enhancers	Dnd41	blood
39	chr14:39640600-39640800	Active TSS	Hela-S3	cervix
40	chr14:39640600-39640800	Enhancers	NHLF	lung
41	chr14:39640600-39641200	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr14:39640600-39641200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr14:39640600-39641200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr14:39640600-39641400	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr14:39640600-39642800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr14:39640600-39643000	Weak transcription	Fetal Intestine Large	intestine
47	chr14:39640600-39643000	Weak transcription	GM12878-XiMat	blood
48	chr14:39640600-39643200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:39640600-39643200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr14:39640600-39643200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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