Variant report

Variant	rs1391557
Chromosome Location	chr1:222809616-222809617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222637300..222641837-chr1:222805384..222811783,8	MCF-7	breast:
2	chr1:222775368..222777772-chr1:222809356..222811917,2	K562	blood:
3	chr1:222809458..222812723-chr1:222815888..222818571,3	MCF-7	breast:
4	chr1:222791343..222795260-chr1:222806268..222810918,6	K562	blood:
5	chr1:222806292..222810839-chr1:222815256..222818233,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234419	Chromatin interaction
ENSG00000154305	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11485123	0.86[EUR][1000 genomes]
rs12063226	0.82[EUR][1000 genomes]
rs1391558	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1498382	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17011666	0.83[AMR][1000 genomes]
rs17011686	0.84[ASN][1000 genomes]
rs1909195	0.83[AMR][1000 genomes]
rs1909197	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2030076	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2088514	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2133188	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270707	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2378604	0.87[EUR][1000 genomes]
rs2936020	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936023	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2936049	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2936051	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2936052	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2936054	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3002129	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3002146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3002148	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008614	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008615	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3008616	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008618	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3008622	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3008625	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3008629	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3008637	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34433664	0.88[EUR][1000 genomes]
rs35507977	0.81[EUR][1000 genomes]
rs3811465	0.88[EUR][1000 genomes]
rs61827168	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9441835	0.82[AMR][1000 genomes]
rs9441926	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222792400-222816600	Weak transcription	Small Intestine	intestine
2	chr1:222792600-222816600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222792600-222817000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:222793200-222816600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:222793200-222816600	Weak transcription	Hela-S3	cervix
6	chr1:222793600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:222794600-222809800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:222794600-222810400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:222794600-222810400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr1:222794600-222813400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:222794600-222813600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:222794600-222814000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:222794600-222815000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:222794800-222813200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:222794800-222813600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:222795400-222810400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:222795400-222810600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:222795400-222810600	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:222795400-222812000	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr1:222795400-222813400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:222795600-222810600	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:222795800-222810600	Strong transcription	Adipose Nuclei	Adipose
23	chr1:222797000-222812400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr1:222797400-222810600	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:222797600-222810600	Strong transcription	Placenta	Placenta
26	chr1:222798400-222812000	Strong transcription	Fetal Stomach	stomach
27	chr1:222799600-222815000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:222801000-222816600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:222801200-222809800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:222801200-222815200	Strong transcription	HSMM	muscle
31	chr1:222801400-222816800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:222801600-222816600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:222801800-222815000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:222802000-222813800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:222802200-222816800	Weak transcription	Stomach Mucosa	stomach
36	chr1:222802400-222816600	Weak transcription	HMEC	breast
37	chr1:222802600-222816600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:222802800-222816600	Weak transcription	GM12878-XiMat	blood
39	chr1:222803000-222816800	Weak transcription	Colonic Mucosa	Colon
40	chr1:222803200-222816400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:222803200-222816600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:222803800-222812800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:222803800-222816600	Weak transcription	NHLF	lung
44	chr1:222804000-222812000	Strong transcription	Osteobl	bone
45	chr1:222804400-222817000	Weak transcription	Fetal Brain Male	brain
46	chr1:222805400-222810800	Strong transcription	K562	blood
47	chr1:222805600-222814200	Weak transcription	HSMMtube	muscle
48	chr1:222805800-222816600	Weak transcription	Fetal Heart	heart
49	chr1:222805800-222817000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:222806400-222816600	Weak transcription	Primary hematopoietic stem cells	blood

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