Variant report

Variant	rs916091
Chromosome Location	chr3:46424007-46424008
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1001007	0.86[ASN][1000 genomes]
rs11266744	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11574433	0.82[AFR][1000 genomes]
rs11575815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11575816	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800023	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800874	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2187673	0.86[ASN][1000 genomes]
rs2187674	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2213290	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254089	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2734225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2734648	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856757	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2856764	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856765	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3181039	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3204849	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34682274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060576	0.86[ASN][1000 genomes]
rs41515644	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4560336	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683223	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441974	0.86[ASN][1000 genomes]
rs66484806	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs746492	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756988	chr3:46419634-46444794	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2759146	chr3:46419634-46444794	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv10267	chr3:46423130-46440713	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46404400-46424600	Weak transcription	Spleen	Spleen
2	chr3:46420400-46425400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:46420400-46427600	Weak transcription	Pancreas	Pancrea
4	chr3:46421400-46426000	Enhancers	Fetal Lung	lung
5	chr3:46421800-46425000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:46422000-46425200	Enhancers	Colonic Mucosa	Colon
7	chr3:46422200-46425400	Enhancers	Stomach Mucosa	stomach
8	chr3:46422200-46435200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:46422400-46424600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:46422400-46424800	Enhancers	Dnd41	blood
11	chr3:46422400-46425400	Weak transcription	Thymus	Thymus
12	chr3:46422400-46426400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:46422400-46427800	Weak transcription	Esophagus	oesophagus
14	chr3:46422400-46438600	Weak transcription	Psoas Muscle	Psoas
15	chr3:46422600-46424400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:46422600-46424600	Weak transcription	Placenta	Placenta
17	chr3:46422600-46424800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr3:46422600-46425000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:46422600-46425000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr3:46422600-46425000	Weak transcription	Brain Substantia Nigra	brain
21	chr3:46422600-46427600	Weak transcription	Hela-S3	cervix
22	chr3:46422600-46435200	Weak transcription	Right Atrium	heart
23	chr3:46422800-46424400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:46422800-46424400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:46422800-46424400	Weak transcription	Fetal Thymus	thymus
26	chr3:46422800-46424600	Weak transcription	GM12878-XiMat	blood
27	chr3:46422800-46424800	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr3:46422800-46424800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr3:46422800-46424800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:46422800-46424800	Weak transcription	HMEC	breast
31	chr3:46422800-46429400	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:46423000-46424200	Weak transcription	Primary B cells from cord blood	blood
33	chr3:46423000-46424400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:46423000-46424400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr3:46423000-46424400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:46423000-46424400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:46423000-46424400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:46423000-46424600	Weak transcription	Brain Anterior Caudate	brain
39	chr3:46423000-46424600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:46423000-46424800	Weak transcription	Brain Hippocampus Middle	brain
41	chr3:46423000-46424800	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr3:46423000-46425000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:46423000-46425200	Weak transcription	Primary T cells from cord blood	blood
44	chr3:46423000-46425200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr3:46423000-46425200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr3:46423000-46425200	Weak transcription	Liver	Liver
47	chr3:46423000-46426400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:46423000-46427600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:46423000-46427600	Weak transcription	HSMM	muscle
50	chr3:46423000-46427600	Weak transcription	HSMMtube	muscle

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