Variant report

Variant	rs10000311
Chromosome Location	chr4:53507945-53507946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53506657..53508794-chr4:53511302..53513850,2	MCF-7	breast:
2	chr4:53507829..53510054-chr4:53552893..53554891,2	K562	blood:
3	chr4:53503939..53505879-chr4:53506758..53508956,2	MCF-7	breast:
4	chr4:53507474..53510349-chr4:53513013..53515386,2	K562	blood:
5	chr4:53494448..53497400-chr4:53507705..53509616,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109189	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10001085	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10001370	0.87[ASN][1000 genomes]
rs10001387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10002261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10003396	0.87[ASN][1000 genomes]
rs10010306	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10012676	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10014740	1.00[CEU][hapmap]
rs10014752	1.00[ASN][1000 genomes]
rs10014850	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[ASN][1000 genomes]
rs10020568	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10021143	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10023867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs10027906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10028085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10028755	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10029145	0.93[ASN][1000 genomes]
rs10031386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10032700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10033218	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10471216	1.00[ASN][1000 genomes]
rs13434726	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13435157	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28376189	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28379922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28380682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28396506	1.00[AMR][1000 genomes]
rs28402205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28411005	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28412170	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28430452	1.00[ASN][1000 genomes]
rs28451750	0.93[ASN][1000 genomes]
rs28475600	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28478374	1.00[AMR][1000 genomes]
rs28482298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28503210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28565016	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28588481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28590396	1.00[ASN][1000 genomes]
rs28619184	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28644292	0.93[ASN][1000 genomes]
rs28654693	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28660571	1.00[ASN][1000 genomes]
rs28672279	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28694544	1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28721897	1.00[ASN][1000 genomes]
rs28722174	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs28784684	1.00[ASN][1000 genomes]
rs28825181	0.90[ASN][1000 genomes]
rs28825412	1.00[ASN][1000 genomes]
rs28849759	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28852068	1.00[ASN][1000 genomes]
rs6830833	1.00[ASN][1000 genomes]
rs7673679	0.90[ASN][1000 genomes]
rs9990686	1.00[ASN][1000 genomes]
rs9994643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9997863	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594201	chr4:52798624-53732445	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1000931	chr4:53420849-53689319	Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv537093	chr4:53420849-53689319	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv948860	chr4:53421172-53675549	Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2754049	chr4:53454272-53539672	Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv524494	chr4:53459620-53582065	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53464200-53523600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:53468200-53510200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:53477600-53510200	Weak transcription	Esophagus	oesophagus
4	chr4:53484600-53508400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr4:53485800-53508400	Weak transcription	Stomach Mucosa	stomach
6	chr4:53486600-53508800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr4:53492200-53510000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr4:53493200-53510400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr4:53494400-53509400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:53494400-53510200	Weak transcription	Lung	lung
11	chr4:53494600-53509400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr4:53496600-53522800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:53500600-53510200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:53500600-53510600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:53502200-53509400	Weak transcription	Liver	Liver
16	chr4:53502600-53509600	Weak transcription	Gastric	stomach
17	chr4:53502600-53510000	Weak transcription	Pancreas	Pancrea
18	chr4:53505400-53510800	Enhancers	Right Atrium	heart
19	chr4:53505800-53517800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:53506000-53510800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr4:53506000-53511200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:53506400-53508200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:53506400-53508400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:53506400-53508800	Enhancers	HMEC	breast
25	chr4:53506400-53510800	Enhancers	Psoas Muscle	Psoas
26	chr4:53506600-53508000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:53506600-53521200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:53506800-53508200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:53506800-53510600	Enhancers	Fetal Lung	lung
30	chr4:53506800-53510600	Enhancers	Ovary	ovary
31	chr4:53507000-53508000	Enhancers	Fetal Muscle Leg	muscle
32	chr4:53507000-53508000	Enhancers	Fetal Stomach	stomach
33	chr4:53507000-53508200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:53507000-53508400	Enhancers	NHDF-Ad	bronchial
35	chr4:53507000-53508800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr4:53507000-53508800	Enhancers	Rectal Smooth Muscle	rectum
37	chr4:53507000-53508800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:53507000-53508800	Flanking Active TSS	GM12878-XiMat	blood
39	chr4:53507000-53508800	Enhancers	NHLF	lung
40	chr4:53507000-53509000	Enhancers	NHEK	skin
41	chr4:53507000-53509800	Enhancers	Stomach Smooth Muscle	stomach
42	chr4:53507000-53514600	Enhancers	Fetal Brain Male	brain
43	chr4:53507200-53508000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr4:53507200-53508000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:53507200-53508000	Enhancers	Adipose Nuclei	Adipose
46	chr4:53507200-53508000	Enhancers	Brain Germinal Matrix	brain
47	chr4:53507200-53508000	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr4:53507200-53508400	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr4:53507200-53508400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:53507200-53508400	Enhancers	HUES6 Cell Line	embryonic stem cell

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