Variant report

Variant	rs7650912
Chromosome Location	chr3:88197859-88197860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:88197832-88197863	MCF-7	breast:	n/a	n/a
2	MXI1	chr3:88197855-88200371	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:88197807-88198045	HepG2	liver:	n/a	n/a
4	POLR2A	chr3:88197680-88199698	SK-N-MC	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:88104745..88109799-chr3:88197543..88201780,9	MCF-7	breast:
2	chr3:88118437..88120288-chr3:88196139..88198741,2	MCF-7	breast:
3	chr3:88197168..88201570-chr3:88204371..88207068,4	K562	blood:
4	chr3:88106502..88110909-chr3:88195834..88201659,8	MCF-7	breast:
5	chr3:88143908..88145953-chr3:88197666..88200045,3	MCF-7	breast:
6	chr3:88197769..88200999-chr3:88203234..88208947,7	MCF-7	breast:
7	chr3:88181347..88191666-chr3:88192147..88201015,17	MCF-7	breast:
8	chr3:88107215..88109971-chr3:88197433..88199191,2	K562	blood:
9	chr3:88197032..88201570-chr3:88203720..88209497,8	K562	blood:

No data

Variant related genes	Relation type
C3orf38	TF binding region
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction
ENSG00000241535	Chromatin interaction
ENSG00000175105	Chromatin interaction
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11128023	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1367615	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1431154	1.00[EUR][1000 genomes]
rs1594453	1.00[EUR][1000 genomes]
rs1594455	1.00[EUR][1000 genomes]
rs1604700	1.00[EUR][1000 genomes]
rs1897238	1.00[EUR][1000 genomes]
rs2033390	1.00[EUR][1000 genomes]
rs2567037	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2735557	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241549	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4241550	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4287925	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4303891	0.85[AFR][1000 genomes]
rs4404474	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4425287	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4443201	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4513473	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4515075	1.00[EUR][1000 genomes]
rs4616669	1.00[EUR][1000 genomes]
rs4858927	1.00[EUR][1000 genomes]
rs4858933	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4858970	1.00[EUR][1000 genomes]
rs4858987	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4858988	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4858989	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6551270	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7615309	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7621357	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7625641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7633215	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7633486	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7636845	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7650749	1.00[EUR][1000 genomes]
rs7650915	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs930154	1.00[EUR][1000 genomes]
rs9310062	1.00[EUR][1000 genomes]
rs9310063	1.00[EUR][1000 genomes]
rs9310069	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9310073	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812903	1.00[EUR][1000 genomes]
rs9833231	1.00[EUR][1000 genomes]
rs9850550	1.00[EUR][1000 genomes]
rs9860113	0.99[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9864564	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9867614	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
2	chr3:88145200-88198200	Weak transcription	Aorta	Aorta
3	chr3:88162800-88198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:88171000-88198000	Weak transcription	Small Intestine	intestine
5	chr3:88171400-88198000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr3:88181000-88198000	Weak transcription	Brain Anterior Caudate	brain
7	chr3:88181000-88198000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:88184200-88198000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:88189400-88198000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:88189800-88198000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:88189800-88198000	Weak transcription	Right Ventricle	heart
12	chr3:88190000-88198000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:88190000-88198200	Weak transcription	Ovary	ovary
14	chr3:88190400-88198000	Weak transcription	Fetal Kidney	kidney
15	chr3:88190400-88198000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr3:88191000-88198000	Weak transcription	Primary B cells from cord blood	blood
17	chr3:88191200-88198000	Weak transcription	Primary T cells from cord blood	blood
18	chr3:88191200-88198200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:88191400-88198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:88191800-88198000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:88191800-88198000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:88192400-88198000	Weak transcription	Osteobl	bone
23	chr3:88196200-88198000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:88196200-88202000	Active TSS	GM12878-XiMat	blood
25	chr3:88196400-88198000	Enhancers	Fetal Intestine Small	intestine
26	chr3:88196400-88198000	Enhancers	HepG2	liver
27	chr3:88196600-88198000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr3:88196600-88198000	Weak transcription	Stomach Mucosa	stomach
29	chr3:88196800-88198200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr3:88197000-88198200	Flanking Active TSS	Dnd41	blood
31	chr3:88197000-88200600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:88197200-88198000	Enhancers	Brain Cingulate Gyrus	brain
33	chr3:88197200-88198200	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr3:88197200-88198200	Enhancers	Colon Smooth Muscle	Colon
35	chr3:88197200-88198400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:88197400-88198000	Enhancers	Brain Substantia Nigra	brain
37	chr3:88197400-88198000	Enhancers	Colonic Mucosa	Colon
38	chr3:88197400-88198000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:88197400-88198000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:88197400-88198000	Enhancers	NH-A	brain
41	chr3:88197400-88201000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:88197600-88198000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr3:88197600-88198000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:88197600-88198000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:88197600-88198000	Weak transcription	Brain Angular Gyrus	brain
46	chr3:88197600-88198000	Enhancers	Brain Hippocampus Middle	brain
47	chr3:88197600-88198000	Enhancers	Duodenum Smooth Muscle	Duodenum
48	chr3:88197600-88198000	Enhancers	Fetal Lung	lung
49	chr3:88197600-88198000	Weak transcription	Right Atrium	heart
50	chr3:88197600-88198000	Flanking Active TSS	Hela-S3	cervix

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