Variant report

Variant	rs4852974
Chromosome Location	chr2:73927931-73927932
allele	A/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
ENSG00000163016	Chromatin interaction
ENSG00000144035	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11689234	0.82[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs12478871	0.91[CHB][hapmap]
rs12991161	0.81[CHB][hapmap]
rs13027816	0.82[CHB][hapmap]
rs2280506	0.81[CHB][hapmap]
rs2280507	0.93[CHB][hapmap]
rs2421586	0.81[CHB][hapmap]
rs2421587	0.81[CHB][hapmap]
rs2947845	0.82[CHB][hapmap]
rs4627598	0.82[CHB][hapmap]
rs4852311	0.93[CHB][hapmap]
rs4852951	0.82[CHB][hapmap]
rs4852954	0.81[CHB][hapmap]
rs6728685	0.81[AFR][1000 genomes]
rs6742619	0.80[EUR][1000 genomes]
rs6744273	0.93[CHB][hapmap]
rs7570683	0.81[CHB][hapmap]
rs7579068	0.81[CHB][hapmap]
rs7607989	0.81[CHB][hapmap]

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
rs4852974	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs4852974	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 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	chr2:73926200-73928000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:73926200-73930600	Enhancers	Fetal Lung	lung
7	chr2:73926400-73928000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:73926600-73928000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:73926600-73929400	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:73926600-73929800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr2:73926800-73928000	Weak transcription	Gastric	stomach
12	chr2:73926800-73929800	Enhancers	Stomach Mucosa	stomach
13	chr2:73927000-73928000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:73927000-73930000	Enhancers	Ovary	ovary
15	chr2:73927000-73931400	Enhancers	Placenta	Placenta
16	chr2:73927200-73928000	Active TSS	Rectal Smooth Muscle	rectum
17	chr2:73927200-73928600	Enhancers	Adipose Nuclei	Adipose
18	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:73927200-73932600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr2:73927200-73932800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:73927400-73928000	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr2:73927400-73928400	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr2:73927400-73928600	Enhancers	Esophagus	oesophagus
24	chr2:73927400-73928600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr2:73927600-73928000	Enhancers	Brain Cingulate Gyrus	brain
26	chr2:73927600-73928200	Enhancers	Brain Hippocampus Middle	brain
27	chr2:73927600-73928400	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr2:73927600-73928400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:73927600-73928600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:73927600-73929800	Enhancers	Colonic Mucosa	Colon
31	chr2:73927600-73929800	Enhancers	Pancreas	Pancrea
32	chr2:73927800-73928000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
33	chr2:73927800-73928000	Enhancers	Stomach Smooth Muscle	stomach
34	chr2:73927800-73928000	Enhancers	K562	blood
35	chr2:73927800-73928400	Flanking Active TSS	Fetal Intestine Large	intestine
36	chr2:73927800-73928400	Enhancers	Right Atrium	heart
37	chr2:73927800-73929200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
38	chr2:73927800-73929800	Enhancers	Fetal Muscle Trunk	muscle
39	chr2:73927800-73930000	Enhancers	Lung	lung
40	chr2:73927800-73954800	Weak transcription	Brain Inferior Temporal Lobe	brain

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