Variant report

Variant	rs10488042
Chromosome Location	chr7:101652458-101652459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:101582848..101590446-chr7:101646237..101653992,20	MCF-7	breast:
2	chr7:101540840..101542361-chr7:101651553..101653872,2	MCF-7	breast:
3	chr7:101642133..101644445-chr7:101650974..101653254,2	MCF-7	breast:
4	chr7:101513034..101514774-chr7:101650619..101652950,2	MCF-7	breast:
5	chr7:101629646..101631231-chr7:101651146..101653804,2	MCF-7	breast:
6	chr7:101457163..101465176-chr7:101645974..101654631,24	MCF-7	breast:
7	chr7:101610580..101623329-chr7:101643563..101654055,32	MCF-7	breast:
8	chr7:101650955..101653343-chr7:101787745..101790282,2	MCF-7	breast:
9	chr7:101645872..101649176-chr7:101651087..101654410,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10231075	1.00[JPT][hapmap]
rs10236615	1.00[JPT][hapmap]
rs10259603	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10274188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10276057	1.00[JPT][hapmap]
rs10488043	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953355	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11975995	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12530931	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534969	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12537526	1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17408612	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17408640	1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs17487076	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17487672	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17494372	0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1882763	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs202142	1.00[JPT][hapmap]
rs202147	1.00[JPT][hapmap]
rs202150	1.00[JPT][hapmap]
rs202152	1.00[JPT][hapmap]
rs2031085	1.00[JPT][hapmap]
rs28461243	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28668902	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs36118129	0.92[ASN][1000 genomes]
rs56392048	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6465839	1.00[JPT][hapmap]
rs67101142	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6973312	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6973714	0.92[ASN][1000 genomes]
rs73185836	0.84[ASN][1000 genomes]
rs73185860	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7780375	0.92[ASN][1000 genomes]
rs7780631	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7785266	1.00[JPT][hapmap]
rs7796818	1.00[JPT][hapmap]
rs7796995	1.00[JPT][hapmap]
rs7799663	1.00[CEU][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7805379	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7810922	1.00[JPT][hapmap]
rs9969318	1.00[JPT][hapmap]

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	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv482521	chr7:101604002-101718950	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv831080	chr7:101629121-101718950	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv981839	chr7:101632578-101663728	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv966867	chr7:101645987-101658423	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101578200-101671200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:101627000-101671200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:101630000-101668000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:101639800-101655800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:101641600-101672000	Weak transcription	K562	blood
6	chr7:101642000-101661600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr7:101642200-101666600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:101642200-101671400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:101642200-101671600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr7:101642200-101674600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:101642400-101661800	Weak transcription	Spleen	Spleen
12	chr7:101642400-101668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr7:101642400-101671200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr7:101642400-101671400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr7:101642400-101675400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:101642800-101668000	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:101642800-101697600	Weak transcription	Primary B cells from cord blood	blood
18	chr7:101643000-101655600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr7:101643000-101657400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr7:101643000-101665200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:101643000-101672800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr7:101643000-101675600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr7:101643200-101666400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:101644000-101652800	Weak transcription	HSMMtube	muscle
25	chr7:101644200-101661800	Weak transcription	Right Atrium	heart
26	chr7:101644400-101657400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr7:101645800-101653600	Strong transcription	Fetal Intestine Small	intestine
28	chr7:101646800-101671600	Weak transcription	GM12878-XiMat	blood
29	chr7:101647200-101662000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:101647600-101655800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:101648200-101652800	Weak transcription	Osteobl	bone
32	chr7:101648200-101656200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr7:101648200-101656200	Weak transcription	Fetal Lung	lung
34	chr7:101648200-101671200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr7:101648200-101681400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr7:101648200-101688000	Weak transcription	Ovary	ovary
37	chr7:101648400-101656000	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:101649000-101666800	Weak transcription	Fetal Muscle Leg	muscle
39	chr7:101649000-101671400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:101649200-101667000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr7:101649400-101666600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr7:101649400-101672800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:101649600-101652600	Weak transcription	Fetal Thymus	thymus
44	chr7:101649600-101665000	Weak transcription	Lung	lung
45	chr7:101649800-101666800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr7:101649800-101671600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:101650600-101657400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr7:101650800-101657600	Weak transcription	Brain Germinal Matrix	brain
49	chr7:101650800-101664600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:101651000-101657200	Weak transcription	NHLF	lung

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