Variant report

Variant	rs2001490
Chromosome Location	chr2:73928098-73928099
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	chr2:73868945..73872912-chr2:73927731..73932752,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf78-1	chr2:73927556-73928129	ENSG00000251346

Variant related genes	Relation type
ENSG00000144035	Chromatin interaction
ENSG00000163016	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10172044	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10191988	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10200762	0.93[EUR][1000 genomes]
rs10208995	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11126414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126415	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11126416	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11126417	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11689234	0.89[CHB][hapmap]
rs11891140	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11892172	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11894953	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12052539	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12053242	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12233112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12233115	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12478871	0.92[CHB][hapmap]
rs12611487	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12612423	0.85[AMR][1000 genomes]
rs12615807	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12619258	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12624267	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12713788	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12713789	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713790	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713791	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713793	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713794	0.84[EUR][1000 genomes]
rs12713795	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12713797	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12713798	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12992607	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12997018	0.84[EUR][1000 genomes]
rs12997568	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12998980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13000788	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13003035	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13005729	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006448	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13006598	0.81[AMR][1000 genomes]
rs13013228	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13014700	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13015885	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13020517	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13022837	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13026192	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13031853	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13031866	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13033744	0.83[AMR][1000 genomes]
rs13383097	0.82[AMR][1000 genomes]
rs17350056	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17350125	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17350188	0.87[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17434634	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17434655	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1806683	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1815028	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2001436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2006997	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2012574	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116367	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs2272051	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs2272178	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2280507	0.82[CHB][hapmap]
rs2421557	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2421558	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2421559	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs2421574	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421575	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2421672	0.83[CEU][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421674	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421675	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421676	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2421677	0.83[EUR][1000 genomes]
rs35421685	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35498419	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35767294	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35791379	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3813228	0.83[CEU][hapmap];0.83[AMR][1000 genomes]
rs3980695	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4241257	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4358149	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4513320	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4530394	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852311	0.82[CHB][hapmap]
rs4852316	0.91[EUR][1000 genomes]
rs4852966	0.88[EUR][1000 genomes]
rs4852967	0.86[EUR][1000 genomes]
rs4852972	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4852975	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4852976	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4852977	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4852978	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732812	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6748233	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6749841	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6750494	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750515	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6750877	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6755500	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7210	0.87[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7368570	0.81[AMR][1000 genomes]
rs7370393	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7558546	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7591112	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7597302	0.80[AMR][1000 genomes]
rs7599453	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7606947	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7608328	0.84[EUR][1000 genomes]
rs891695	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9309475	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9309476	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv874277	chr2:73870010-73931971	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874278	chr2:73870010-73931971	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv3340115	chr2:73870416-73930142	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2762675	chr2:73875799-73928886	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv441760	chr2:73875799-73928886	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv3426494	chr2:73876125-73939153	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv3460808	chr2:73877074-73940302	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv3460809	chr2:73877074-73940302	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv829461	chr2:73877427-73931225	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv2753082	chr2:73891045-73955545	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv979022	chr2:73897805-73932073	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	esv34157	chr2:73901718-73949151	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
20	nsv998315	chr2:73919185-74003998	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
21	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
22	nsv1003153	chr2:73927235-73975416	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats 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 target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2001490	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs2001490	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73900600-73954800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:73902200-73931400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:73926000-73929400	Enhancers	Liver	Liver
4	chr2:73926000-73931000	Enhancers	Fetal Intestine Small	intestine
5	chr2:73926200-73930600	Enhancers	Fetal Lung	lung
6	chr2:73926600-73929400	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:73926600-73929800	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr2:73926800-73929800	Enhancers	Stomach Mucosa	stomach
9	chr2:73927000-73930000	Enhancers	Ovary	ovary
10	chr2:73927000-73931400	Enhancers	Placenta	Placenta
11	chr2:73927200-73928600	Enhancers	Adipose Nuclei	Adipose
12	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells	blood
13	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:73927200-73932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:73927400-73928400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr2:73927400-73928600	Enhancers	Esophagus	oesophagus
17	chr2:73927400-73928600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr2:73927600-73928200	Enhancers	Brain Hippocampus Middle	brain
19	chr2:73927600-73928400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr2:73927600-73928400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr2:73927600-73928600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr2:73927600-73929800	Enhancers	Colonic Mucosa	Colon
23	chr2:73927600-73929800	Enhancers	Pancreas	Pancrea
24	chr2:73927800-73928400	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr2:73927800-73928400	Enhancers	Right Atrium	heart
26	chr2:73927800-73929200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
27	chr2:73927800-73929800	Enhancers	Fetal Muscle Trunk	muscle
28	chr2:73927800-73930000	Enhancers	Lung	lung
29	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr2:73928000-73928200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr2:73928000-73928400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:73928000-73928400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:73928000-73928400	Enhancers	Left Ventricle	heart
34	chr2:73928000-73928400	Flanking Active TSS	K562	blood
35	chr2:73928000-73929600	Enhancers	Gastric	stomach
36	chr2:73928000-73930200	Enhancers	Fetal Kidney	kidney
37	chr2:73928000-73930600	Weak transcription	Brain Cingulate Gyrus	brain

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