Variant report

Variant	rs670008
Chromosome Location	chr3:100322660-100322661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100322090..100322923-chr3:100479827..100480358,2	MCF-7	breast:
2	chr3:100322114..100322780-chr3:100353316..100353989,3	MCF-7	breast:
3	chr3:100321992..100322818-chr3:100353419..100354308,2	MCF-7	breast:
4	chr3:100321003..100323549-chr3:100347554..100350487,3	MCF-7	breast:
5	chr3:100322069..100322963-chr3:100515153..100515789,2	MCF-7	breast:
6	chr3:100322209..100326377-chr3:100427335..100430667,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114354	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10755119	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1143774	1.00[CHB][hapmap]
rs1144105	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1144106	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1144107	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1144108	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1144122	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1144124	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1144125	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs1144126	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1145348	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1165264	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs11921801	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11921907	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs1305374	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1384198	0.81[CEU][hapmap]
rs1676343	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs1676369	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718272	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1718279	0.81[CEU][hapmap];1.00[CHB][hapmap]
rs1842730	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1842731	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126540	0.83[CEU][hapmap]
rs4088588	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4144968	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs4928070	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs55677333	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs560803	1.00[CHB][hapmap]
rs56239206	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586347	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs591728	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs604047	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs610854	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs62274583	0.83[ASN][1000 genomes]
rs6441357	0.84[EUR][1000 genomes]
rs6441383	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs6441384	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs653947	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667609	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767460	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6770559	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6779489	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788891	0.81[CEU][hapmap]
rs6789364	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs694612	0.89[CEU][hapmap]
rs73143117	0.88[EUR][1000 genomes]
rs900234	1.00[CHB][hapmap]
rs900235	0.81[CEU][hapmap]
rs9864288	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs9878163	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751965	chr3:100299310-100462527	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	esv2751966	chr3:100299310-100468500	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv2756284	chr3:100299329-100427937	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752830	chr3:100299329-100442478	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv432464	chr3:100299329-100442478	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv2751967	chr3:100299329-100455139	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv2751968	chr3:100299329-100476713	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv432466	chr3:100299329-100476713	Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv536667	chr3:100308355-100445857	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv460770	chr3:100310812-100433592	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv591150	chr3:100310812-100433592	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv2763708	chr3:100317928-100442509	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
14	nsv591151	chr3:100322043-100433592	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100318200-100324200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:100318800-100323200	Enhancers	HMEC	breast
3	chr3:100319000-100323000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:100319800-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:100320200-100322800	Enhancers	NHEK	skin
6	chr3:100320600-100323000	Enhancers	Fetal Intestine Small	intestine
7	chr3:100320800-100323000	Enhancers	Fetal Intestine Large	intestine
8	chr3:100321000-100322800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:100321200-100322800	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:100321200-100322800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:100321200-100322800	Enhancers	Stomach Mucosa	stomach
12	chr3:100321200-100322800	Enhancers	HSMMtube	muscle
13	chr3:100321200-100322800	Enhancers	K562	blood
14	chr3:100321200-100323000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:100321400-100322800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr3:100321400-100322800	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:100321400-100322800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr3:100321400-100322800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:100321400-100322800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:100321400-100322800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:100321400-100324200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:100321600-100322800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr3:100321600-100323000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:100321800-100323000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr3:100322000-100322800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:100322000-100322800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:100322200-100322800	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:100322200-100322800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:100322200-100322800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
30	chr3:100322200-100322800	Enhancers	Primary T cells fromperipheralblood	blood
31	chr3:100322200-100322800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr3:100322200-100322800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr3:100322200-100322800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:100322200-100322800	Enhancers	Colonic Mucosa	Colon
35	chr3:100322200-100322800	Enhancers	Fetal Thymus	thymus
36	chr3:100322200-100322800	Enhancers	Small Intestine	intestine
37	chr3:100322200-100322800	Flanking Active TSS	GM12878-XiMat	blood
38	chr3:100322400-100322800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr3:100322400-100322800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:100322400-100322800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:100322400-100322800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:100322400-100322800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr3:100322400-100322800	Enhancers	HepG2	liver
44	chr3:100322400-100323000	Enhancers	Primary T cells from cord blood	blood
45	chr3:100322400-100323000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr3:100322400-100323000	Enhancers	A549	lung
47	chr3:100322600-100322800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:100322600-100322800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:100322600-100322800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:100322600-100322800	Enhancers	Primary B cells from cord blood	blood

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