Variant report

Variant	rs2378583
Chromosome Location	chr1:222739300-222739301
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222737305..222739948-chr1:222766255..222768391,2	K562	blood:
2	chr1:222739220..222742946-chr1:222744858..222747647,3	K562	blood:
3	chr1:222735935..222738524-chr1:222739039..222741294,2	K562	blood:
4	chr1:222735227..222738969-chr1:222739039..222743402,4	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11485178	0.83[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11485180	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11487813	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1319392	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1603742	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17163214	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1909192	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1995152	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2133185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173401	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936027	1.00[ASW][hapmap];0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936031	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936034	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936035	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936037	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2936038	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2936040	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2936048	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3002151	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3008641	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008644	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3008650	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4400619	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv1842070	chr1:222732027-222763235	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222720800-222742400	Weak transcription	NHLF	lung
2	chr1:222720800-222757400	Weak transcription	HSMMtube	muscle
3	chr1:222721200-222762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:222721800-222762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:222722000-222745000	Weak transcription	Hela-S3	cervix
6	chr1:222722000-222755600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:222722000-222755800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:222723800-222742400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:222724800-222750800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:222725600-222762200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr1:222727600-222762600	Weak transcription	Aorta	Aorta
12	chr1:222727800-222762400	Weak transcription	Thymus	Thymus
13	chr1:222728000-222744400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:222728200-222762200	Weak transcription	Small Intestine	intestine
15	chr1:222728600-222744400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:222728800-222746400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:222729600-222762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:222729800-222758800	Weak transcription	Pancreas	Pancrea
19	chr1:222730200-222742000	Weak transcription	HepG2	liver
20	chr1:222730400-222742800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:222730800-222741800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr1:222730800-222741800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:222730800-222760200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:222730800-222761200	Weak transcription	Fetal Brain Male	brain
25	chr1:222731200-222742200	Weak transcription	Osteobl	bone
26	chr1:222731200-222762400	Weak transcription	Spleen	Spleen
27	chr1:222731600-222742200	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:222731600-222742200	Weak transcription	Fetal Stomach	stomach
29	chr1:222731600-222745200	Weak transcription	Fetal Intestine Small	intestine
30	chr1:222731600-222748600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:222731600-222756200	Weak transcription	Esophagus	oesophagus
32	chr1:222731600-222758800	Weak transcription	Gastric	stomach
33	chr1:222731600-222762200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:222731800-222743200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:222733200-222745000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr1:222733600-222739600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:222733600-222739600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:222733600-222762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:222733800-222741800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:222733800-222761800	Weak transcription	Brain Angular Gyrus	brain
41	chr1:222733800-222762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:222734000-222739800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:222734000-222741800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:222734000-222762400	Weak transcription	Right Ventricle	heart
45	chr1:222734200-222741800	Weak transcription	Brain Germinal Matrix	brain
46	chr1:222734200-222742000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:222734200-222762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr1:222734600-222742000	Weak transcription	HMEC	breast
49	chr1:222734800-222741800	Weak transcription	Brain Hippocampus Middle	brain
50	chr1:222734800-222750200	Weak transcription	HUVEC	blood vessel

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