Variant report

Variant	rs12611687
Chromosome Location	chr2:99918561-99918562
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11123782	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11685870	0.87[AMR][1000 genomes]
rs11686535	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11687328	0.87[AMR][1000 genomes]
rs11892472	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11895206	0.85[AMR][1000 genomes]
rs11897443	0.86[AMR][1000 genomes]
rs13008948	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13009863	0.83[AMR][1000 genomes]
rs13011240	0.85[AMR][1000 genomes]
rs13014360	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13016182	0.87[AMR][1000 genomes]
rs13019192	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13026997	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6732397	0.85[AMR][1000 genomes]
rs74177687	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570978	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
7	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
14	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	nsv1004291	chr2:99855978-99919999	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
17	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
18	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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
19	nsv961843	chr2:99916605-99924549	Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12611687	REV1	cis	Thyroid	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99879000-99933600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr2:99892400-99918600	Weak transcription	Brain Anterior Caudate	brain
3	chr2:99892400-99935000	Weak transcription	Brain Angular Gyrus	brain
4	chr2:99894200-99934800	Weak transcription	Gastric	stomach
5	chr2:99895400-99935000	Weak transcription	Pancreas	Pancrea
6	chr2:99895800-99921000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:99895800-99933600	Weak transcription	HSMM	muscle
8	chr2:99895800-99933600	Weak transcription	HSMMtube	muscle
9	chr2:99896800-99933400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:99897000-99933600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:99897200-99933800	Weak transcription	Fetal Intestine Small	intestine
12	chr2:99897400-99933800	Weak transcription	HepG2	liver
13	chr2:99897600-99918800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr2:99898200-99918800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:99898200-99934000	Weak transcription	Small Intestine	intestine
16	chr2:99898400-99938600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:99898600-99933800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:99899400-99918600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:99899400-99933800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:99899600-99918600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:99899600-99933000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:99899800-99935000	Weak transcription	Esophagus	oesophagus
23	chr2:99900000-99933600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:99900400-99933800	Weak transcription	Colonic Mucosa	Colon
25	chr2:99901000-99918600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:99901200-99933400	Weak transcription	Primary B cells from cord blood	blood
27	chr2:99901200-99936600	Weak transcription	Fetal Brain Male	brain
28	chr2:99901400-99918800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:99901400-99922800	Weak transcription	Ovary	ovary
30	chr2:99901600-99918600	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:99901600-99918600	Weak transcription	Psoas Muscle	Psoas
32	chr2:99901600-99918600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:99901600-99919800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:99901600-99933400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:99901600-99933600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr2:99901600-99933600	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr2:99901600-99933800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:99901600-99933800	Weak transcription	Fetal Intestine Large	intestine
39	chr2:99901600-99941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:99901800-99918600	Weak transcription	Fetal Stomach	stomach
41	chr2:99901800-99919000	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:99902800-99918600	Weak transcription	Fetal Muscle Leg	muscle
43	chr2:99907800-99933800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:99908000-99918600	Weak transcription	Adipose Nuclei	Adipose
45	chr2:99908000-99918600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr2:99908000-99934200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:99908200-99918600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:99908200-99919000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:99908400-99918600	Weak transcription	Brain Substantia Nigra	brain
50	chr2:99908400-99918600	Weak transcription	Stomach Smooth Muscle	stomach

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