Variant report

Variant	rs6677908
Chromosome Location	chr1:227068049-227068050
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	REST	chr1:227067931-227068615	PANC-1	pancreas:	n/a	chr1:227068137-227068155
2	REST	chr1:227068043-227068490	H1-hESC	embryonic stem cell:	n/a	chr1:227068137-227068155
3	REST	chr1:227068013-227068546	MCF-7	breast:	n/a	chr1:227068137-227068155
4	REST	chr1:227068047-227068439	A549	lung:	n/a	chr1:227068137-227068155
5	REST	chr1:227067911-227068546	PFSK-1	brain:	n/a	chr1:227068137-227068155
6	REST	chr1:227068017-227068467	SK-N-SH	brain:	n/a	chr1:227068137-227068155
7	REST	chr1:227068044-227068476	K562	blood:	n/a	chr1:227068137-227068155
8	REST	chr1:227068005-227068540	MCF-7	breast:	n/a	chr1:227068137-227068155
9	REST	chr1:227067890-227068624	ECC-1	luminal epithelium:	n/a	chr1:227068137-227068155
10	BCL3	chr1:227068008-227068477	GM12878	blood:	n/a	n/a
11	REST	chr1:227067956-227068641	ECC-1	luminal epithelium:	n/a	chr1:227068137-227068155
12	REST	chr1:227067983-227068616	HL-60	blood:	n/a	chr1:227068137-227068155
13	TEAD4	chr1:227068044-227068491	A549	lung:	n/a	n/a
14	REST	chr1:227068012-227068525	HCT-116	colon:	n/a	chr1:227068137-227068155
15	REST	chr1:227067960-227068489	PFSK-1	brain:	n/a	chr1:227068137-227068155

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227067713..227070080-chr1:227071671..227073358,2	K562	blood:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000143801	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12069540	0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1341281	1.00[EUR][1000 genomes]
rs1341282	1.00[EUR][1000 genomes]
rs16846590	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4520384	1.00[EUR][1000 genomes]
rs57594469	1.00[EUR][1000 genomes]
rs58698650	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58973334	1.00[EUR][1000 genomes]
rs59683545	1.00[EUR][1000 genomes]
rs59692841	1.00[EUR][1000 genomes]
rs60294511	1.00[EUR][1000 genomes]
rs60560949	1.00[EUR][1000 genomes]
rs61103575	1.00[EUR][1000 genomes]
rs61185121	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426539	1.00[EUR][1000 genomes]
rs6426540	1.00[EUR][1000 genomes]
rs6671059	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678839	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74139805	1.00[EUR][1000 genomes]
rs74139806	1.00[EUR][1000 genomes]
rs7522645	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523790	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555672	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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227059200-227069000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:227059400-227069600	Weak transcription	Primary B cells from cord blood	blood
3	chr1:227059600-227068400	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:227059600-227069200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:227059600-227070200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr1:227059800-227070200	Weak transcription	Osteobl	bone
7	chr1:227059800-227075600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:227059800-227095000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:227060000-227068200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:227060000-227068200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:227060000-227068400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:227060000-227068800	Weak transcription	NHDF-Ad	bronchial
13	chr1:227060000-227069400	Weak transcription	Esophagus	oesophagus
14	chr1:227060000-227069600	Weak transcription	Right Atrium	heart
15	chr1:227060000-227069800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:227060000-227070000	Weak transcription	Small Intestine	intestine
17	chr1:227060000-227070600	Weak transcription	Fetal Brain Male	brain
18	chr1:227060200-227070200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr1:227060400-227068400	Weak transcription	Colon Smooth Muscle	Colon
20	chr1:227060400-227069200	Weak transcription	GM12878-XiMat	blood
21	chr1:227060400-227073800	Weak transcription	HepG2	liver
22	chr1:227060400-227077600	Weak transcription	Brain Germinal Matrix	brain
23	chr1:227060600-227068400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:227060600-227070400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:227060600-227070400	Weak transcription	HUVEC	blood vessel
26	chr1:227060600-227077400	Weak transcription	Fetal Brain Female	brain
27	chr1:227061200-227069800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr1:227062200-227077400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:227062400-227073000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:227062400-227073000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:227062800-227068400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:227063000-227081400	Weak transcription	Psoas Muscle	Psoas
33	chr1:227063200-227069800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:227063400-227070200	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:227063600-227069800	Strong transcription	Fetal Stomach	stomach
36	chr1:227063600-227070200	Weak transcription	Fetal Lung	lung
37	chr1:227063800-227069800	Weak transcription	Colonic Mucosa	Colon
38	chr1:227063800-227070000	Weak transcription	Fetal Kidney	kidney
39	chr1:227063800-227078000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr1:227064000-227068200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:227064000-227070000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr1:227064000-227070200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr1:227064000-227070400	Weak transcription	NH-A	brain
44	chr1:227064000-227072600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr1:227064200-227068800	Strong transcription	Adipose Nuclei	Adipose
46	chr1:227064200-227069800	Weak transcription	Stomach Mucosa	stomach
47	chr1:227064200-227070600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:227064200-227070600	Weak transcription	Hela-S3	cervix
49	chr1:227064400-227069200	Strong transcription	Left Ventricle	heart
50	chr1:227064400-227069600	Strong transcription	Lung	lung

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