Variant report

Variant	rs1269643
Chromosome Location	chr7:107887960-107887961
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107886563..107889560-chr7:107893965..107897090,3	MCF-7	breast:
2	chr7:107887211..107889896-chr7:108095081..108098683,4	MCF-7	breast:
3	chr7:107885764..107888071-chr7:107990459..107993788,3	MCF-7	breast:
4	chr7:107885444..107889446-chr7:107936320..107941216,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091129	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1155	0.89[CEU][hapmap];0.84[AMR][1000 genomes]
rs11772445	0.85[LWK][hapmap]
rs12537654	0.85[LWK][hapmap]
rs1269621	0.85[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]
rs1269622	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1269623	0.89[EUR][1000 genomes]
rs1269625	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1269628	0.89[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1269629	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1269634	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269639	0.92[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269641	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1269642	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1269645	0.96[CEU][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1269649	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1269650	0.81[GIH][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes]
rs1269651	0.81[MKK][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes]
rs1269652	0.81[EUR][1000 genomes]
rs1269653	0.81[EUR][1000 genomes]
rs1269655	0.84[AMR][1000 genomes]
rs1269656	0.84[AMR][1000 genomes]
rs1269659	0.89[CEU][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes]
rs2284280	0.85[LWK][hapmap];0.88[MKK][hapmap]
rs36065373	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs370133	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs3819747	0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs394145	0.85[LWK][hapmap]
rs405945	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs409724	0.81[MKK][hapmap]
rs409797	0.81[MKK][hapmap]
rs422011	0.96[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6970096	0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs926146	0.92[CHB][hapmap];1.00[JPT][hapmap]

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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107884800-107890600	Weak transcription	Brain Substantia Nigra	brain
2	chr7:107885600-107888400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr7:107885600-107889400	Enhancers	Osteobl	bone
4	chr7:107885800-107888400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:107886000-107891200	Enhancers	Pancreatic Islets	Pancreatic Islet
6	chr7:107886200-107889400	Enhancers	HMEC	breast
7	chr7:107886200-107889600	Enhancers	HUVEC	blood vessel
8	chr7:107886400-107888000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:107886400-107888400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr7:107886400-107888400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr7:107886400-107888400	Enhancers	NHEK	skin
12	chr7:107886600-107889400	Enhancers	NH-A	brain
13	chr7:107886800-107888600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr7:107886800-107889000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:107886800-107890200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:107887200-107888200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:107887200-107888400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr7:107887200-107888800	Weak transcription	Fetal Kidney	kidney
19	chr7:107887200-107889000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr7:107887200-107889200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:107887200-107890600	Weak transcription	Right Atrium	heart
22	chr7:107887200-107891800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:107887400-107888200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr7:107887400-107888400	Enhancers	HSMM	muscle
25	chr7:107887400-107888600	Enhancers	K562	blood
26	chr7:107887400-107889000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:107887400-107889800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr7:107887400-107890200	Weak transcription	Fetal Intestine Small	intestine
29	chr7:107887400-107892000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:107887400-107892000	Weak transcription	Pancreas	Pancrea
31	chr7:107887400-107893800	Weak transcription	Fetal Muscle Leg	muscle
32	chr7:107887400-107894000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:107887400-107925000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr7:107887600-107888000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:107887600-107888200	Enhancers	A549	lung
36	chr7:107887600-107889000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr7:107887600-107889000	Weak transcription	Brain Anterior Caudate	brain
38	chr7:107887600-107889000	Weak transcription	HepG2	liver
39	chr7:107887600-107889400	Weak transcription	Psoas Muscle	Psoas
40	chr7:107887600-107890600	Weak transcription	Esophagus	oesophagus
41	chr7:107887800-107888200	Weak transcription	Fetal Intestine Large	intestine
42	chr7:107887800-107888200	Weak transcription	HSMMtube	muscle
43	chr7:107887800-107888400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:107887800-107889000	Weak transcription	Brain Hippocampus Middle	brain
45	chr7:107887800-107889400	Weak transcription	NHDF-Ad	bronchial
46	chr7:107887800-107894000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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