Variant report

Variant	rs6954109
Chromosome Location	chr7:103841764-103841765
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103826587..103829336-chr7:103841216..103843346,2	K562	blood:
2	chr7:103839265..103844326-chr7:103845849..103850093,7	K562	blood:
3	chr7:103831421..103833734-chr7:103840628..103842889,2	MCF-7	breast:
4	chr7:103839347..103842114-chr7:103842519..103845580,4	K562	blood:
5	chr7:103839985..103843508-chr7:103846553..103850027,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164815	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10155973	0.89[AFR][1000 genomes]
rs1019312	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10234499	1.00[EUR][1000 genomes]
rs10235130	1.00[EUR][1000 genomes]
rs10235201	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10241191	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10242752	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10249033	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10250235	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10251308	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10251561	1.00[EUR][1000 genomes]
rs10251976	0.91[AFR][1000 genomes]
rs10255806	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10256764	1.00[EUR][1000 genomes]
rs10258773	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10260238	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs10262560	1.00[EUR][1000 genomes]
rs10262796	0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10262996	0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10263828	1.00[EUR][1000 genomes]
rs10266337	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10267412	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10267940	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10268209	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10270562	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10271923	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10275484	1.00[EUR][1000 genomes]
rs10275705	0.89[AFR][1000 genomes]
rs10276243	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10277637	0.86[YRI][hapmap]
rs10278320	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10279736	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10281709	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10282300	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10487184	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10487192	0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11489610	0.91[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11972422	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11979390	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11979993	0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11980018	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12112576	1.00[EUR][1000 genomes]
rs16873387	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17158586	1.00[EUR][1000 genomes]
rs17159290	0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17159774	1.00[EUR][1000 genomes]
rs2307409	1.00[EUR][1000 genomes]
rs2385134	1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28481813	1.00[EUR][1000 genomes]
rs28577267	0.83[AMR][1000 genomes]
rs28644319	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28645598	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28686914	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28702500	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28773535	1.00[EUR][1000 genomes]
rs28820003	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3779515	0.83[YRI][hapmap]
rs3779516	0.84[YRI][hapmap]
rs58842751	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59750244	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6948021	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6949887	0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs6962621	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6967711	1.00[EUR][1000 genomes]
rs6975642	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73413894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73415704	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73415717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73415730	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73415786	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73415801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73417705	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73417718	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7777446	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7777906	0.91[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7810496	1.00[EUR][1000 genomes]
rs9655777	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9656090	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103767200-103843600	Weak transcription	Right Ventricle	heart
2	chr7:103796400-103843600	Weak transcription	Fetal Brain Male	brain
3	chr7:103797200-103847000	Weak transcription	Fetal Heart	heart
4	chr7:103816000-103846200	Weak transcription	Stomach Mucosa	stomach
5	chr7:103822000-103845400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:103826400-103844400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr7:103826800-103844600	Strong transcription	Adipose Nuclei	Adipose
8	chr7:103827400-103844600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:103831600-103844400	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr7:103831800-103842200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr7:103831800-103844200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr7:103831800-103844400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:103831800-103844400	Strong transcription	Fetal Lung	lung
14	chr7:103832800-103846600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr7:103833800-103844800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:103834000-103844400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:103834400-103844600	Strong transcription	Liver	Liver
18	chr7:103834600-103844600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr7:103834800-103844600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr7:103835200-103844200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr7:103835400-103844200	Strong transcription	Placenta	Placenta
22	chr7:103835600-103844200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr7:103835800-103844200	Strong transcription	Primary T cells from cord blood	blood
24	chr7:103836600-103844400	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr7:103836800-103844400	Strong transcription	HSMM	muscle
26	chr7:103836800-103844800	Strong transcription	A549	lung
27	chr7:103837000-103844000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr7:103837000-103844400	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr7:103837200-103844400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr7:103837200-103844600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:103837200-103844600	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr7:103837400-103843200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:103837400-103844400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr7:103837400-103844400	Strong transcription	Colon Smooth Muscle	Colon
35	chr7:103837600-103844400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:103837800-103844200	Strong transcription	Osteobl	bone
37	chr7:103838000-103844600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:103838200-103844200	Strong transcription	Muscle Satellite Cultured Cells	--
39	chr7:103838200-103844200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr7:103838400-103841800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr7:103838400-103841800	Strong transcription	Spleen	Spleen
42	chr7:103838400-103844200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr7:103838400-103844200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr7:103838400-103844600	Strong transcription	Brain Substantia Nigra	brain
45	chr7:103838400-103844800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr7:103838600-103841800	ZNF genes & repeats	GM12878-XiMat	blood
47	chr7:103838600-103843000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:103838600-103843600	Strong transcription	Psoas Muscle	Psoas
49	chr7:103838600-103844000	Strong transcription	Left Ventricle	heart
50	chr7:103838600-103844000	Strong transcription	Rectal Smooth Muscle	rectum

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