Variant report

Variant	rs2315840
Chromosome Location	chr3:99829320-99829321
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99826567..99829453-chr3:99832757..99834371,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction
ENSG00000184220	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10049383	0.81[CHB][hapmap]
rs1017968	0.86[CHB][hapmap]
rs10212525	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs1021341	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs10511177	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs13064704	0.81[CHB][hapmap]
rs13069311	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs13323143	0.81[CHB][hapmap]
rs1489816	0.90[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs16841920	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1688766	0.88[CHD][hapmap]
rs4075038	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs4361315	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs4571265	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs61255658	0.81[EUR][1000 genomes]
rs6790535	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs6790877	0.86[CHB][hapmap]
rs6799379	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs6802422	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs6806178	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs6807176	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs7610486	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs7620228	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs7627991	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs923470	0.81[CHB][hapmap]
rs923471	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9814359	0.81[CHB][hapmap]
rs9815439	0.81[CHB][hapmap]
rs9823908	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9828079	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9829705	0.82[ASW][hapmap]
rs9833888	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9833980	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9841186	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9851645	0.81[CHB][hapmap]
rs9864437	0.81[CHB][hapmap];0.92[CHD][hapmap]
rs9873709	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs9873878	0.81[CHB][hapmap]
rs9875640	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99795800-99866600	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99818000-99836600	Weak transcription	Primary B cells from cord blood	blood
3	chr3:99823600-99837200	Weak transcription	Pancreas	Pancrea
4	chr3:99825200-99835000	Weak transcription	K562	blood
5	chr3:99825200-99840600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:99825200-99844000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:99825200-99844200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:99825600-99841000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:99826000-99833200	Weak transcription	Ovary	ovary
10	chr3:99826200-99838200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:99826400-99832000	Weak transcription	Right Ventricle	heart
12	chr3:99826600-99862600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:99827400-99839000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:99827600-99829800	Weak transcription	Gastric	stomach
15	chr3:99827800-99829400	Weak transcription	Fetal Kidney	kidney
16	chr3:99827800-99832000	Weak transcription	Left Ventricle	heart
17	chr3:99827800-99833000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:99827800-99834200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr3:99828000-99830200	Weak transcription	Colon Smooth Muscle	Colon
20	chr3:99828000-99832200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:99828400-99829600	Weak transcription	Psoas Muscle	Psoas
22	chr3:99828400-99833000	Weak transcription	HepG2	liver
23	chr3:99829000-99829400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr3:99829200-99829400	Flanking Active TSS	Aorta	Aorta
25	chr3:99829200-99829400	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr3:99829200-99829400	Enhancers	HSMMtube	muscle
27	chr3:99829200-99833200	Active TSS	Right Atrium	heart
28	chr3:99829200-99841000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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