Variant report

Variant	rs3779516
Chromosome Location	chr7:103847464-103847465
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:103846497..103848385-chr7:103909952..103912269,2	MCF-7	breast:
2	chr7:103628555..103630772-chr7:103847007..103849982,2	K562	blood:
3	chr7:103846124..103848372-chr7:103861589..103863576,2	MCF-7	breast:
4	chr7:103847011..103848620-chr7:142657967..142659467,2	MCF-7	breast:
5	chr7:103833753..103835540-chr7:103846175..103847854,2	K562	blood:

Variant related genes	Relation type
ENSG00000189056	Chromatin interaction
ENSG00000197993	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1019312	0.83[YRI][hapmap]
rs10241191	0.84[YRI][hapmap]
rs10255806	0.83[YRI][hapmap]
rs10260238	0.83[YRI][hapmap]
rs10262796	0.83[YRI][hapmap]
rs10262996	0.83[YRI][hapmap]
rs10267412	0.84[YRI][hapmap]
rs10271923	0.84[YRI][hapmap]
rs10276243	0.84[YRI][hapmap]
rs10278320	0.84[YRI][hapmap]
rs10281709	0.87[YRI][hapmap]
rs10282300	0.84[YRI][hapmap]
rs10487184	0.83[YRI][hapmap]
rs10487190	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10487191	1.00[CEU][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes]
rs10487192	0.91[YRI][hapmap]
rs11764162	0.99[EUR][1000 genomes]
rs11767680	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11771050	0.97[EUR][1000 genomes]
rs11771108	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11771398	0.96[EUR][1000 genomes]
rs11773044	0.96[EUR][1000 genomes]
rs11773664	0.99[EUR][1000 genomes]
rs11979993	0.83[YRI][hapmap]
rs16873387	0.84[YRI][hapmap]
rs17159290	0.91[YRI][hapmap]
rs17324174	0.81[EUR][1000 genomes]
rs17326187	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17327021	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17327119	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17377164	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17377990	0.80[EUR][1000 genomes]
rs2014811	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2058722	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs2299405	0.81[EUR][1000 genomes]
rs2299406	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2299410	0.93[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2299414	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2385134	0.83[YRI][hapmap]
rs2385142	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3779515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3779517	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3808003	1.00[CEU][hapmap];0.83[JPT][hapmap]
rs3808004	0.96[EUR][1000 genomes]
rs3808017	0.81[EUR][1000 genomes]
rs4141408	0.81[EUR][1000 genomes]
rs56950973	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6954109	0.84[YRI][hapmap]
rs6961789	0.83[EUR][1000 genomes]
rs6964461	0.81[EUR][1000 genomes]
rs6975642	0.84[YRI][hapmap]
rs6977598	0.81[EUR][1000 genomes]
rs73189317	0.81[EUR][1000 genomes]
rs73191412	0.96[EUR][1000 genomes]
rs73191421	0.96[EUR][1000 genomes]
rs7777446	0.84[YRI][hapmap]
rs7804341	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807600	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9655777	0.86[YRI][hapmap]
rs9656090	0.84[YRI][hapmap]

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	chr7:103840000-103847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:103840400-103847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:103840600-103847800	Weak transcription	Small Intestine	intestine
4	chr7:103843800-103847600	Weak transcription	Aorta	Aorta
5	chr7:103844000-103847600	Weak transcription	Gastric	stomach
6	chr7:103844200-103847600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:103846200-103847600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:103846200-103847600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:103846200-103847600	Flanking Active TSS	Dnd41	blood
10	chr7:103846200-103847800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:103846200-103847800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr7:103846200-103847800	Enhancers	Spleen	Spleen
13	chr7:103846200-103849200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr7:103846200-103849400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:103846400-103847800	Flanking Active TSS	Liver	Liver
16	chr7:103846400-103849400	Active TSS	A549	lung
17	chr7:103846600-103848000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:103846600-103849000	Active TSS	K562	blood
19	chr7:103846600-103849400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr7:103846800-103847600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr7:103846800-103847600	Enhancers	Primary B cells from peripheral blood	blood
22	chr7:103846800-103847600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr7:103846800-103847600	Flanking Active TSS	Hela-S3	cervix
24	chr7:103846800-103847600	Flanking Active TSS	HMEC	breast
25	chr7:103846800-103847800	Flanking Active TSS	NHEK	skin
26	chr7:103846800-103848000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:103846800-103848200	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr7:103846800-103849200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr7:103847000-103847600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:103847000-103847600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:103847000-103847600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:103847000-103847600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr7:103847000-103847600	Flanking Active TSS	Fetal Brain Female	brain
34	chr7:103847000-103847600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr7:103847000-103847600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr7:103847000-103847600	Flanking Active TSS	NHDF-Ad	bronchial
37	chr7:103847000-103847600	Flanking Active TSS	Osteobl	bone
38	chr7:103847000-103847800	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr7:103847000-103847800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr7:103847000-103847800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr7:103847000-103847800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr7:103847000-103847800	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr7:103847000-103847800	Flanking Active TSS	Duodenum Mucosa	Duodenum
44	chr7:103847000-103847800	Flanking Active TSS	Fetal Heart	heart
45	chr7:103847000-103847800	Flanking Active TSS	Fetal Lung	lung
46	chr7:103847000-103847800	Flanking Active TSS	HUVEC	blood vessel
47	chr7:103847000-103848000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr7:103847000-103848000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr7:103847000-103848000	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr7:103847000-103848000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

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