Variant report

Variant	rs6966259
Chromosome Location	chr7:107884135-107884136
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:107883815..107886718-chr7:108095136..108097625,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10224607	1.00[CEU][hapmap]
rs10257555	1.00[CEU][hapmap]
rs10464622	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10464623	0.95[EUR][1000 genomes]
rs10464625	0.95[EUR][1000 genomes]
rs10464626	0.95[EUR][1000 genomes]
rs10464627	0.90[EUR][1000 genomes]
rs10464628	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12531903	1.00[CEU][hapmap]
rs12665964	0.91[EUR][1000 genomes]
rs12667098	0.95[EUR][1000 genomes]
rs12667131	0.95[EUR][1000 genomes]
rs12667151	0.95[EUR][1000 genomes]
rs12667206	0.95[EUR][1000 genomes]
rs12669568	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12671199	0.85[EUR][1000 genomes]
rs12672376	0.90[EUR][1000 genomes]
rs12674151	0.95[EUR][1000 genomes]
rs12674313	0.81[EUR][1000 genomes]
rs16872446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs16872448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16872465	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];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16872472	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16872481	1.00[CEU][hapmap]
rs17155207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155277	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155280	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17155316	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17155345	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs17155362	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17155369	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2072320	1.00[EUR][1000 genomes]
rs2272618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2284279	1.00[CEU][hapmap]
rs2284281	1.00[CEU][hapmap]
rs2299988	1.00[CEU][hapmap]
rs2299998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2300001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2300004	1.00[EUR][1000 genomes]
rs2300005	1.00[EUR][1000 genomes]
rs2300006	1.00[EUR][1000 genomes]
rs2300007	0.95[EUR][1000 genomes]
rs2300008	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2300009	0.95[EUR][1000 genomes]
rs2300010	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs2300011	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3750140	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3753152	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3801929	1.00[CEU][hapmap]
rs3817670	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55772998	1.00[EUR][1000 genomes]
rs58432175	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58523350	1.00[EUR][1000 genomes]
rs58799340	1.00[EUR][1000 genomes]
rs59173255	1.00[EUR][1000 genomes]
rs60503554	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61040788	1.00[EUR][1000 genomes]
rs61057696	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67456250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67592649	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67940074	0.95[EUR][1000 genomes]
rs6956041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6956711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6964394	1.00[EUR][1000 genomes]
rs6970634	0.86[EUR][1000 genomes]
rs6978117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73199578	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73199594	0.95[EUR][1000 genomes]
rs73199595	0.95[EUR][1000 genomes]
rs73199599	0.95[EUR][1000 genomes]
rs73199600	0.95[EUR][1000 genomes]
rs73201503	1.00[EUR][1000 genomes]
rs73201504	1.00[EUR][1000 genomes]
rs73201511	1.00[EUR][1000 genomes]
rs73201512	1.00[EUR][1000 genomes]
rs73201513	1.00[EUR][1000 genomes]
rs73201515	1.00[EUR][1000 genomes]
rs73414373	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73727511	0.95[EUR][1000 genomes]
rs73727512	0.95[EUR][1000 genomes]
rs7777092	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7777322	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7783944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7784319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7784353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7785181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7796457	1.00[EUR][1000 genomes]
rs9641405	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv949344	chr7:107396502-107987085	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv831090	chr7:107786650-108011196	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107830400-107886400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr7:107860600-107886600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:107871200-107886400	Weak transcription	Brain Anterior Caudate	brain
4	chr7:107874800-107886200	Weak transcription	HSMMtube	muscle
5	chr7:107876400-107886400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:107877000-107885600	Weak transcription	HSMM	muscle
7	chr7:107877000-107886200	Weak transcription	HMEC	breast
8	chr7:107877800-107884600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr7:107877800-107884600	Weak transcription	Fetal Intestine Small	intestine
10	chr7:107877800-107886400	Weak transcription	Pancreas	Pancrea
11	chr7:107878400-107885200	Weak transcription	Fetal Intestine Large	intestine
12	chr7:107880400-107884400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr7:107880400-107886200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:107880600-107884600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:107880600-107884600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:107880600-107885200	Weak transcription	K562	blood
17	chr7:107880600-107887000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr7:107880800-107886600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:107881000-107886200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:107881200-107884400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr7:107881200-107886000	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:107881200-107886400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr7:107881200-107886400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:107881200-107886400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr7:107881200-107886400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr7:107881200-107886600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:107881600-107884600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr7:107881800-107886400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:107883600-107886800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:107884000-107884400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr7:107884000-107884400	Enhancers	A549	lung

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