Variant report

Variant	rs12930702
Chromosome Location	chr16:72077000-72077001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72076599..72078294-chr16:72087307..72089388,2	K562	blood:
2	chr16:72072556..72075421-chr16:72076238..72078955,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TXNL4B-1	chr16:72076843-72077017	NONHSAT143544

Variant related genes	Relation type
ENSG00000261701	Chromatin interaction
ENSG00000257017	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10048144	0.83[AMR][1000 genomes]
rs10492813	0.80[ASN][1000 genomes]
rs10492814	0.81[ASN][1000 genomes]
rs1050361	0.81[ASN][1000 genomes]
rs12162087	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12443622	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12446480	0.91[ASN][1000 genomes]
rs12708925	0.80[ASN][1000 genomes]
rs12917999	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12924413	0.81[ASN][1000 genomes]
rs12928365	0.82[EUR][1000 genomes]
rs12930205	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12932845	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12935266	0.89[EUR][1000 genomes]
rs2070937	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2081222	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2081223	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2236765	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2241411	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2287998	0.89[ASN][1000 genomes]
rs2287999	0.89[ASN][1000 genomes]
rs2288000	0.89[ASN][1000 genomes]
rs2288001	0.89[ASN][1000 genomes]
rs2288002	0.91[ASN][1000 genomes]
rs2303285	0.81[ASN][1000 genomes]
rs251033	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550035	0.85[ASN][1000 genomes]
rs2550038	0.86[ASN][1000 genomes]
rs2550868	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2550869	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2550870	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2550876	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3764311	0.81[ASN][1000 genomes]
rs3764314	0.81[ASN][1000 genomes]
rs3812986	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3852781	0.81[ASN][1000 genomes]
rs3852782	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3852784	0.85[EUR][1000 genomes]
rs3890860	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3909542	0.82[EUR][1000 genomes]
rs4788458	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4788461	0.88[EUR][1000 genomes]
rs4788609	0.88[EUR][1000 genomes]
rs4788610	0.90[EUR][1000 genomes]
rs56139130	0.93[ASN][1000 genomes]
rs6499557	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499563	0.87[EUR][1000 genomes]
rs7185840	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7186155	0.87[EUR][1000 genomes]
rs7188962	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7189115	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7189591	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7190994	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7194397	0.81[ASN][1000 genomes]
rs7197020	0.81[EUR][1000 genomes]
rs7199261	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7200003	0.84[EUR][1000 genomes]
rs7200854	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7201643	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7201866	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7202268	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7203426	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7203821	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7350838	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7940	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8053907	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs8059437	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8060770	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8182213	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9924964	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9926927	0.81[ASN][1000 genomes]
rs9927526	0.84[EUR][1000 genomes]
rs9928157	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9930890	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9932951	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9938382	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72051400-72078600	Weak transcription	Fetal Kidney	kidney
2	chr16:72058200-72077000	Weak transcription	Colonic Mucosa	Colon
3	chr16:72058200-72078000	Weak transcription	Fetal Lung	lung
4	chr16:72059600-72084600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr16:72060000-72079200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr16:72060200-72080000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:72060200-72095600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr16:72060200-72110600	Weak transcription	Esophagus	oesophagus
9	chr16:72062200-72079600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr16:72062200-72080000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr16:72062400-72078000	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr16:72062600-72079800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr16:72063800-72079800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr16:72075000-72077800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr16:72075200-72077600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr16:72075200-72078400	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr16:72075400-72077400	Strong transcription	Primary B cells from peripheral blood	blood
18	chr16:72075400-72077400	Strong transcription	Brain Substantia Nigra	brain
19	chr16:72075400-72078000	Strong transcription	Brain Hippocampus Middle	brain
20	chr16:72075600-72077400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr16:72075600-72077400	Enhancers	Pancreas	Pancrea
22	chr16:72075600-72077400	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr16:72075600-72077400	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr16:72075600-72078400	Strong transcription	Aorta	Aorta
25	chr16:72075600-72079600	Enhancers	HepG2	liver
26	chr16:72075800-72077400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr16:72075800-72077600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr16:72075800-72077800	Strong transcription	Brain Germinal Matrix	brain
29	chr16:72075800-72078000	Strong transcription	Primary B cells from cord blood	blood
30	chr16:72075800-72078000	Strong transcription	Fetal Brain Female	brain
31	chr16:72075800-72078000	Strong transcription	Ovary	ovary
32	chr16:72075800-72078200	Strong transcription	Brain Anterior Caudate	brain
33	chr16:72075800-72078400	Strong transcription	Primary T cells from cord blood	blood
34	chr16:72075800-72078600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr16:72076000-72077000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr16:72076000-72077000	Genic enhancers	Right Ventricle	heart
37	chr16:72076000-72077400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr16:72076000-72077400	Enhancers	Psoas Muscle	Psoas
39	chr16:72076000-72077400	Genic enhancers	Stomach Smooth Muscle	stomach
40	chr16:72076000-72078000	Strong transcription	Thymus	Thymus
41	chr16:72076000-72078200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr16:72076200-72078000	Strong transcription	Fetal Intestine Small	intestine
43	chr16:72076200-72078200	Strong transcription	Brain Angular Gyrus	brain
44	chr16:72076200-72078400	Strong transcription	Fetal Stomach	stomach
45	chr16:72076200-72098200	Weak transcription	Fetal Heart	heart
46	chr16:72076400-72077200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr16:72076400-72078000	Weak transcription	Rectal Smooth Muscle	rectum
48	chr16:72076400-72079200	Weak transcription	Colon Smooth Muscle	Colon
49	chr16:72076600-72077000	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr16:72076600-72077600	Weak transcription	Gastric	stomach

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