Variant report

Variant	rs6780397
Chromosome Location	chr3:52767599-52767600
allele	C/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	KAP1	chr3:52766897-52767904	K562	blood:	n/a	chr3:52767605-52767613
2	ZNF274	chr3:52767187-52767709	GM12878	blood:	n/a	n/a
3	SETDB1	chr3:52767044-52767869	U2OS	brain:	n/a	n/a
4	ZNF274	chr3:52767138-52767694	NT2-D1	testis:	n/a	n/a
5	ZNF274	chr3:52767124-52767741	GM08714	blood:	n/a	n/a
6	ZNF274	chr3:52766685-52768072	K562	blood:	n/a	n/a
7	ZNF274	chr3:52767170-52767746	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52766545..52769494-chr3:52804406..52806680,2	K562	blood:

Variant related genes	Relation type
ENSG00000270941	TF binding region
ENSG00000114904	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11510435	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12107484	1.00[EUR][1000 genomes]
rs17052357	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17052404	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1963813	0.95[AFR][1000 genomes]
rs34173244	1.00[EUR][1000 genomes]
rs4532127	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56134416	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56156188	1.00[EUR][1000 genomes]
rs56276589	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56665533	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57008939	1.00[EUR][1000 genomes]
rs57298447	1.00[EUR][1000 genomes]
rs57757646	1.00[EUR][1000 genomes]
rs57789542	1.00[EUR][1000 genomes]
rs57869735	1.00[EUR][1000 genomes]
rs57946083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58409398	1.00[EUR][1000 genomes]
rs58528592	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58564212	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59638016	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59869286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60040519	1.00[EUR][1000 genomes]
rs60058353	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60256157	1.00[EUR][1000 genomes]
rs60311166	1.00[EUR][1000 genomes]
rs60770874	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60830326	1.00[EUR][1000 genomes]
rs61220667	1.00[EUR][1000 genomes]
rs61538294	1.00[EUR][1000 genomes]
rs6445536	1.00[EUR][1000 genomes]
rs6762788	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6769720	1.00[EUR][1000 genomes]
rs6780005	0.87[EUR][1000 genomes]
rs6803492	0.84[AFR][1000 genomes]
rs72950424	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72950432	1.00[EUR][1000 genomes]
rs72950437	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960212	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960237	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960240	1.00[EUR][1000 genomes]
rs72960260	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72960281	1.00[EUR][1000 genomes]
rs72960285	1.00[EUR][1000 genomes]
rs72965177	1.00[EUR][1000 genomes]
rs72965181	1.00[EUR][1000 genomes]
rs73839126	1.00[EUR][1000 genomes]
rs73839129	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7645785	1.00[EUR][1000 genomes]
rs764636	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7647992	1.00[EUR][1000 genomes]
rs934839	0.88[AFR][1000 genomes];1.00[EUR][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	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv508219	chr3:52741193-52803899	Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52741600-52804000	Weak transcription	Psoas Muscle	Psoas
2	chr3:52742200-52768800	Weak transcription	Colon Smooth Muscle	Colon
3	chr3:52742400-52771400	Weak transcription	K562	blood
4	chr3:52742400-52772800	Weak transcription	Pancreas	Pancrea
5	chr3:52749000-52771600	Weak transcription	Colonic Mucosa	Colon
6	chr3:52749200-52779800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52749400-52776200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:52756200-52777400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:52759600-52768000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:52761200-52770200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:52761600-52781000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:52761600-52802400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:52762000-52770000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:52762000-52787000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:52762200-52767600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:52762400-52772200	Weak transcription	Thymus	Thymus
17	chr3:52762600-52776000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:52763400-52768600	Strong transcription	Fetal Muscle Leg	muscle
19	chr3:52763400-52770200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:52763600-52769400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:52763800-52768400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr3:52763800-52769000	Strong transcription	Left Ventricle	heart
23	chr3:52763800-52769200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:52763800-52769600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
25	chr3:52763800-52770200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:52763800-52788400	Strong transcription	Fetal Brain Female	brain
27	chr3:52763800-52802600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:52764000-52800200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:52764000-52802800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:52764200-52768000	ZNF genes & repeats	Primary B cells from cord blood	blood
31	chr3:52764200-52769800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:52764200-52770000	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr3:52764200-52770200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr3:52764200-52770200	Strong transcription	Duodenum Mucosa	Duodenum
35	chr3:52764200-52770400	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:52764200-52772000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:52764200-52774200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:52764400-52767600	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:52764400-52770200	Strong transcription	Brain Angular Gyrus	brain
40	chr3:52764400-52776000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:52764400-52802600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:52764800-52781600	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr3:52764800-52789400	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:52765200-52768200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:52765200-52789400	Strong transcription	Adipose Nuclei	Adipose
46	chr3:52765200-52793400	Strong transcription	Fetal Intestine Large	intestine
47	chr3:52765400-52767600	Strong transcription	Spleen	Spleen
48	chr3:52765400-52768000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:52765400-52768000	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr3:52765400-52770200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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