Variant report

Variant	rs1640823
Chromosome Location	chr1:223313304-223313305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:223313276-223313326	AoSMC	blood vessel:	n/a
2	chr1:223313276-223313326	K562	blood:	n/a
3	chr1:223313276-223313326	GM06990	blood:	n/a
4	chr1:223313276-223313326	PANC-1	pancreas:	n/a
5	chr1:223313276-223313326	NT2-D1	testis:	n/a
6	chr1:223313276-223313326	ovcar-3	ovarian:	n/a
7	chr1:223313276-223313326	HCF	heart:	n/a
8	chr1:223313276-223313326	SKMC	muscle:	n/a
9	chr1:223313276-223313326	H1-hESC	embryonic stem cell:	embryo
10	chr1:223313276-223313326	GM19239	blood:	n/a
11	chr1:223313276-223313326	GM12878	blood:	n/a
12	chr1:223313276-223313326	BE2_C	brain:	n/a
13	chr1:223313276-223313326	RPTEC	kidney:	n/a
14	chr1:223313276-223313326	AG04450	lung:	fetal
15	chr1:223313276-223313326	HIPEpiC	eye:	n/a
16	chr1:223313276-223313326	Hepatocyte	liver:	n/a
17	chr1:223313276-223313326	HRCEpiC	kidney:	n/a
18	chr1:223313276-223313326	HL-60	blood:	n/a
19	chr1:223313276-223313326	AG04449	skin:	fetal
20	chr1:223313276-223313326	CMK	blood:	n/a
21	chr1:223313276-223313326	SAEC	small airway:	n/a
22	chr1:223313276-223313326	NHDF-neo	bronchial:	n/a
23	chr1:223313276-223313326	HEEpiC	esophagus:	n/a
24	chr1:223313276-223313326	SK-N-MC	brain:	n/a
25	chr1:223313276-223313326	HepG2	liver:	n/a
26	chr1:223313276-223313326	HCT-116	colon:	n/a
27	chr1:223313276-223313326	Caco-2	colon:	n/a
28	chr1:223313276-223313326	SK-N-SH	brain:	n/a
29	chr1:223313276-223313326	HRE	kidney:	n/a
30	chr1:223313276-223313326	HEK293	kidney:	embryo
31	chr1:223313276-223313326	NB4	blood:	n/a
32	chr1:223313276-223313326	U87	brain:	n/a
33	chr1:223313276-223313326	MCF10A-Er-Src	breast:	n/a
34	chr1:223313276-223313326	ECC-1	luminal epithelium:	n/a
35	chr1:223313276-223313326	HCPEpiC	choroid plexus:	n/a
36	chr1:223313276-223313326	PFSK-1	brain:	n/a
37	chr1:223313276-223313326	PrEC	prostate:	n/a
38	chr1:223313276-223313326	IMR90	lung:	fetal
39	chr1:223313276-223313326	AG10803	skin:	n/a
40	chr1:223313276-223313326	GM12892	blood:	n/a
41	chr1:223313276-223313326	Jurkat	blood:	n/a
42	chr1:223313276-223313326	NHBE	bronchial:	n/a
43	chr1:223313276-223313326	HPAEpiC	pulmonary alveolar:	n/a
44	chr1:223313276-223313326	ProgFib	skin:	n/a
45	chr1:223313276-223313326	GM12891	blood:	n/a
46	chr1:223313276-223313326	T-47D	breast:	n/a
47	chr1:223313276-223313326	BJ	skin:	n/a
48	chr1:223313276-223313326	HMEC	breast:	n/a
49	chr1:223313276-223313326	HCM	heart:	n/a
50	chr1:223313276-223313326	Hela-S3	cervix:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223311533..223314395-chr1:223314636..223318058,5	K562	blood:
2	chr1:223295440..223297086-chr1:223310909..223313590,2	MCF-7	breast:

No data

Variant related genes	Relation type
TLR5	CpG island
ENSG00000236846	CpG island
ENSG00000187554	Chromatin interaction
ENSG00000236846	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10489492	0.98[ASN][1000 genomes]
rs11486079	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11488549	0.80[AMR][1000 genomes]
rs1361642	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418145	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1418146	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1612398	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1640803	0.91[ASN][1000 genomes]
rs1640809	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1640811	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640812	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640813	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640814	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640815	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1640816	0.95[ASN][1000 genomes]
rs1640817	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1640818	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1640819	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1640820	0.98[ASN][1000 genomes]
rs17163741	0.80[AMR][1000 genomes]
rs17163742	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17163743	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1773738	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773744	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773749	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773753	0.91[ASN][1000 genomes]
rs1773754	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1773761	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773762	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773763	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773765	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1773766	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773767	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1773768	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935305	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241095	0.84[ASN][1000 genomes]
rs2256707	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2302597	0.98[ASN][1000 genomes]
rs2353474	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2430400	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487834	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2487836	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34136554	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34552707	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34970812	0.83[EUR][1000 genomes]
rs35349967	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35579200	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35705006	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35802580	0.80[AMR][1000 genomes]
rs35953839	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4393150	0.80[AMR][1000 genomes]
rs45501199	0.84[ASN][1000 genomes]
rs5744135	0.84[ASN][1000 genomes]
rs5744138	0.84[ASN][1000 genomes]
rs5744139	0.84[ASN][1000 genomes]
rs5744140	0.84[ASN][1000 genomes]
rs5744143	0.84[ASN][1000 genomes]
rs5744145	0.84[ASN][1000 genomes]
rs5744147	0.84[ASN][1000 genomes]
rs5744149	0.84[ASN][1000 genomes]
rs66553000	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs66662427	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66757010	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66832195	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66938974	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67573944	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67623966	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67639934	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs67833495	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67883821	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs723961	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72743851	0.98[ASN][1000 genomes]
rs72743852	0.95[ASN][1000 genomes]
rs73118159	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73118168	0.91[ASN][1000 genomes]
rs759303	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs988241	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs988242	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs988243	0.80[AMR][1000 genomes]
rs988244	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs988779	0.93[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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
3	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
4	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:223308800-223314000	Weak transcription	Gastric	stomach
6	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
7	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
10	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
12	chr1:223309400-223316000	Weak transcription	NHLF	lung
13	chr1:223309600-223314600	Weak transcription	Ovary	ovary
14	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:223309800-223313600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:223309800-223314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:223310600-223314000	Weak transcription	Esophagus	oesophagus
20	chr1:223310600-223314000	Weak transcription	Psoas Muscle	Psoas
21	chr1:223310600-223314200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:223310600-223315400	Weak transcription	Lung	lung
23	chr1:223311000-223314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:223311200-223314000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:223311200-223314000	Weak transcription	NHDF-Ad	bronchial
26	chr1:223311200-223314200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:223311200-223314200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:223311200-223314400	Weak transcription	HMEC	breast
29	chr1:223311200-223314400	Weak transcription	NHEK	skin
30	chr1:223311200-223314600	Weak transcription	Stomach Mucosa	stomach
31	chr1:223311200-223315800	Weak transcription	Hela-S3	cervix
32	chr1:223311200-223316000	Weak transcription	Liver	Liver
33	chr1:223311400-223314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:223311400-223314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
36	chr1:223311600-223313800	Weak transcription	Placenta	Placenta
37	chr1:223311600-223313800	Weak transcription	Fetal Thymus	thymus
38	chr1:223311600-223314000	Weak transcription	Adipose Nuclei	Adipose
39	chr1:223311600-223314000	Weak transcription	Brain Anterior Caudate	brain
40	chr1:223311600-223314000	Weak transcription	Fetal Lung	lung
41	chr1:223311600-223314200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:223311600-223315600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
44	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:223312000-223314000	Weak transcription	Fetal Stomach	stomach
46	chr1:223312600-223314200	Genic enhancers	Primary monocytes fromperipheralblood	blood
47	chr1:223312600-223315000	Genic enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:223312800-223314000	Weak transcription	Primary B cells from cord blood	blood
49	chr1:223312800-223314200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:223313000-223313400	Genic enhancers	Fetal Muscle Leg	muscle

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