Variant report

Variant	rs3770415
Chromosome Location	chr2:53901477-53901478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53894424..53897447-chr2:53898122..53902216,4	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10185375	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs10210726	0.82[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs12612589	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs12612737	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12612895	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12613682	0.82[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs12614610	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616124	0.87[EUR][1000 genomes]
rs12617315	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12617360	0.82[EUR][1000 genomes]
rs12617668	0.89[EUR][1000 genomes]
rs12618833	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12621547	0.80[ASN][1000 genomes]
rs12621557	0.87[EUR][1000 genomes]
rs12621635	0.82[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs13415842	0.85[EUR][1000 genomes]
rs13421512	0.84[EUR][1000 genomes]
rs17045114	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs17045116	0.86[ASN][1000 genomes]
rs17045125	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs17045215	0.82[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2009149	0.93[EUR][1000 genomes]
rs2058953	0.98[ASN][1000 genomes]
rs2272249	0.82[JPT][hapmap]
rs2287344	0.82[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2287345	0.82[JPT][hapmap]
rs2287512	0.92[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2357491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357492	0.96[ASN][1000 genomes]
rs35833242	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770401	0.82[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs3770410	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3770412	0.92[ASN][1000 genomes]
rs4361164	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56189833	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66684820	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67073722	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6716301	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6760101	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68123661	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7595713	0.82[CEU][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs991599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs994484	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs997644	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

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:71 , 50 per page) page: 1 2

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	chr2:53885600-53925000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:53885800-53911800	Weak transcription	Adipose Nuclei	Adipose
5	chr2:53888200-53934200	Weak transcription	Lung	lung
6	chr2:53888400-53935200	Weak transcription	Fetal Brain Male	brain
7	chr2:53888600-53935200	Weak transcription	Hela-S3	cervix
8	chr2:53889000-53935800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:53892600-53902600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:53892600-53918800	Weak transcription	Left Ventricle	heart
11	chr2:53893400-53915200	Weak transcription	Ovary	ovary
12	chr2:53893800-53926800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:53894200-53920800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:53894400-53912200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:53894400-53914400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr2:53894400-53925000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:53894400-53933800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:53894600-53911200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:53895000-53911800	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:53895400-53919000	Weak transcription	Fetal Intestine Large	intestine
21	chr2:53895400-53921200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr2:53895400-53925800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:53895400-53926200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:53895600-53914800	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr2:53895600-53921400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr2:53895800-53916800	Weak transcription	Brain Anterior Caudate	brain
27	chr2:53895800-53926200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:53896000-53913000	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:53896000-53918800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:53896200-53911200	Weak transcription	Liver	Liver
31	chr2:53896200-53918400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:53896400-53926000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr2:53896800-53910200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr2:53896800-53910800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:53896800-53918800	Weak transcription	Fetal Brain Female	brain
36	chr2:53896800-53924800	Weak transcription	Thymus	Thymus
37	chr2:53896800-53936600	Weak transcription	Aorta	Aorta
38	chr2:53897000-53910400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:53897000-53911400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr2:53897400-53910200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr2:53897400-53910200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:53897400-53912000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr2:53897600-53911600	Weak transcription	Dnd41	blood
44	chr2:53897800-53910800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:53897800-53911000	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr2:53897800-53911600	Weak transcription	Fetal Thymus	thymus
47	chr2:53898000-53910200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr2:53898000-53910200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:53898000-53914800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:53898000-53918800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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