Variant report

Variant	rs2229308
Chromosome Location	chr3:120500446-120500447
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11708525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11708642	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11712360	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713594	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714216	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11716584	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11718363	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719207	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11719896	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11720353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs167722	0.83[CEU][hapmap]
rs17183618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17184204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17243218	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17243933	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2292170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34319994	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34565470	0.84[ASN][1000 genomes]
rs41365345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55663109	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55697401	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55869122	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56140323	0.87[ASN][1000 genomes]
rs6438590	0.84[ASN][1000 genomes]
rs6769985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73183728	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73183730	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637037	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7647895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1005396	chr3:120460741-120580319	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1012541	chr3:120482402-120580319	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv1014477	chr3:120482402-120583166	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	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	chr3:120462800-120503000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:120463000-120502000	Weak transcription	Colonic Mucosa	Colon
3	chr3:120463000-120504200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr3:120463000-120504800	Weak transcription	Fetal Brain Male	brain
5	chr3:120463400-120503000	Weak transcription	Small Intestine	intestine
6	chr3:120482200-120505200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:120482200-120517600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120483200-120509800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:120483400-120502000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:120483400-120521200	Weak transcription	Fetal Heart	heart
11	chr3:120486000-120505000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:120486200-120501600	Strong transcription	Primary B cells from cord blood	blood
13	chr3:120486200-120502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:120486400-120502000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:120487200-120502000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:120487600-120503000	Weak transcription	Right Ventricle	heart
17	chr3:120487800-120501400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:120488600-120503200	Weak transcription	Psoas Muscle	Psoas
19	chr3:120489000-120501600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:120489400-120502000	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:120489600-120501600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:120489600-120502200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:120491600-120502000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:120491600-120511000	Weak transcription	HMEC	breast
25	chr3:120492000-120501600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:120492400-120510600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr3:120493200-120501600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:120493400-120501600	Strong transcription	Primary T cells from cord blood	blood
29	chr3:120493400-120501600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:120493400-120503400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:120494400-120511000	Weak transcription	K562	blood
32	chr3:120495200-120503400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:120495400-120501400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:120495400-120510200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:120495600-120504600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:120496200-120500800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:120496200-120502600	Weak transcription	Brain Anterior Caudate	brain
38	chr3:120496200-120510200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:120496400-120502400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:120496600-120506200	Weak transcription	Fetal Brain Female	brain
41	chr3:120497400-120500600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:120497600-120501200	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:120497600-120501600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:120497800-120501600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:120497800-120501600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:120498200-120501600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:120498200-120501800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr3:120498400-120501800	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:120498400-120501800	Strong transcription	Dnd41	blood
50	chr3:120498600-120501600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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