Variant report

Variant	rs13408029
Chromosome Location	chr2:53928465-53928466
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:53926842..53929678-chr2:54004293..54006164,2	K562	blood:
2	chr2:53927372..53929338-chr2:53931727..53933877,2	K562	blood:
3	chr2:53926965..53929338-chr2:53930911..53933227,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10490468	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11897282	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11901698	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1232	0.91[CHB][hapmap]
rs17045176	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs17045203	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs17520505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17521008	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2008082	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2287340	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2302797	0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2542572	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2542573	0.85[ASN][1000 genomes]
rs2542578	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542580	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2542581	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2542582	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2542583	0.82[ASN][1000 genomes]
rs2542589	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2542590	0.87[ASN][1000 genomes]
rs2542591	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2542592	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2543629	0.82[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2692512	0.83[ASN][1000 genomes]
rs2692513	0.83[ASN][1000 genomes]
rs2692519	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2692521	0.84[ASN][1000 genomes]
rs2692522	0.85[ASN][1000 genomes]
rs2692523	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2692533	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2909262	0.81[ASN][1000 genomes]
rs2949813	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs35772199	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3770394	0.91[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770395	0.92[ASN][1000 genomes]
rs3770397	0.89[ASN][1000 genomes]
rs3770399	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3770411	0.82[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs4116709	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55897904	0.87[ASN][1000 genomes]
rs56214822	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58326257	0.85[ASN][1000 genomes]
rs62137565	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62137573	0.93[ASN][1000 genomes]
rs62137602	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137605	0.82[ASN][1000 genomes]
rs62137606	0.92[ASN][1000 genomes]
rs62137610	0.85[ASN][1000 genomes]
rs62137611	0.85[ASN][1000 genomes]
rs62137612	0.85[ASN][1000 genomes]
rs6730006	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs719127	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72901256	0.93[ASN][1000 genomes]
rs7558968	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7600817	0.92[ASN][1000 genomes]
rs805435	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs805437	0.91[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916267	chr2:53747525-53955999	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv984439	chr2:53861720-53955437	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1011449	chr2:53894529-53947781	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1009107	chr2:53896767-53946913	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1014949	chr2:53896767-53947781	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1011400	chr2:53899956-53947781	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53874200-53935000	Weak transcription	Pancreas	Pancrea
2	chr2:53881400-53934400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:53888200-53934200	Weak transcription	Lung	lung
4	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
5	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
6	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:53896800-53936600	Weak transcription	Aorta	Aorta
9	chr2:53898000-53957400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:53898200-53935400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:53898200-53935400	Weak transcription	Fetal Kidney	kidney
12	chr2:53900600-53935600	Weak transcription	K562	blood
13	chr2:53900800-53936400	Weak transcription	NH-A	brain
14	chr2:53900800-53936800	Weak transcription	NHLF	lung
15	chr2:53906600-53933800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:53906800-53935200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:53908600-53982200	Weak transcription	Small Intestine	intestine
18	chr2:53909000-53934400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:53909000-53935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr2:53910000-53935200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr2:53910000-53941600	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:53910600-53933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:53911400-53935400	Weak transcription	Right Ventricle	heart
26	chr2:53911600-53936200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr2:53912400-53936200	Weak transcription	Gastric	stomach
28	chr2:53912600-53933600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:53913000-53936200	Weak transcription	Spleen	Spleen
30	chr2:53914200-53934800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:53917600-53936200	Weak transcription	Esophagus	oesophagus
32	chr2:53917800-53934000	Weak transcription	Ovary	ovary
33	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
34	chr2:53919000-53935800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:53921800-53933600	Weak transcription	Brain Anterior Caudate	brain
36	chr2:53921800-53933800	Weak transcription	Brain Angular Gyrus	brain
37	chr2:53921800-53935800	Weak transcription	Brain Substantia Nigra	brain
38	chr2:53922400-53935200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:53923400-53929400	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr2:53924200-53934400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr2:53924400-53935400	Weak transcription	Colonic Mucosa	Colon
42	chr2:53925000-53936200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:53925200-53935200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr2:53925200-53935400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:53925400-53933600	Weak transcription	Fetal Intestine Small	intestine
46	chr2:53925400-53933600	Weak transcription	Fetal Stomach	stomach
47	chr2:53925400-53935800	Weak transcription	A549	lung
48	chr2:53925400-53979400	Weak transcription	Psoas Muscle	Psoas
49	chr2:53926000-53935800	Weak transcription	HSMMtube	muscle
50	chr2:53926800-53936000	Weak transcription	Brain Hippocampus Middle	brain

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