Variant report

Variant	rs11942547
Chromosome Location	chr4:148870791-148870792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:148870240..148873199-chr4:148874453..148876510,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11934409	0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11937178	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11939997	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11941546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11946732	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs13434578	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13435747	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17024137	1.00[CEU][hapmap]
rs17024143	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17024182	1.00[CEU][hapmap]
rs187006	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2118033	0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2118035	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2164530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2164531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2358180	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2358181	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2575585	1.00[CEU][hapmap]
rs2635256	0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2635266	0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2635267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635268	0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4337713	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs55752555	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67913037	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72617450	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7655265	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7666206	0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7669783	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs7672161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7685779	1.00[CEU][hapmap]
rs975371	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs975372	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024596	chr4:148830472-148886915	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148797400-148879600	Weak transcription	Gastric	stomach
2	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
3	chr4:148833600-148877400	Weak transcription	Small Intestine	intestine
4	chr4:148847400-148877200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:148849200-148875600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:148850000-148876400	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr4:148850200-148890800	Weak transcription	HUVEC	blood vessel
8	chr4:148855400-148884800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:148856400-148889000	Weak transcription	Placenta	Placenta
10	chr4:148859400-148898000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:148859800-148878600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:148860800-148879200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:148861800-148878400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr4:148861800-148883000	Weak transcription	Lung	lung
15	chr4:148861800-148883000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:148861800-148884800	Weak transcription	Esophagus	oesophagus
17	chr4:148861800-148885400	Weak transcription	Pancreas	Pancrea
18	chr4:148861800-148890800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr4:148862000-148878400	Weak transcription	Fetal Heart	heart
20	chr4:148862000-148879200	Weak transcription	Psoas Muscle	Psoas
21	chr4:148862800-148887800	Weak transcription	Fetal Intestine Large	intestine
22	chr4:148864200-148877000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:148864200-148887200	Weak transcription	NHLF	lung
24	chr4:148864400-148873000	Weak transcription	Fetal Kidney	kidney
25	chr4:148864400-148896800	Weak transcription	Osteobl	bone
26	chr4:148864600-148876800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr4:148864800-148891200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr4:148865000-148879400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr4:148865400-148873400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr4:148865400-148879400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr4:148865600-148871400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr4:148865800-148871000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr4:148865800-148873000	Strong transcription	Fetal Muscle Leg	muscle
34	chr4:148866000-148873600	Strong transcription	Adipose Nuclei	Adipose
35	chr4:148866200-148874400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr4:148866400-148872800	Weak transcription	Fetal Lung	lung
37	chr4:148866400-148887400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr4:148866400-148889800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:148866400-148927400	Weak transcription	Thymus	Thymus
40	chr4:148866600-148882800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr4:148866800-148871000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:148867000-148873200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:148867200-148873600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr4:148867200-148891200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr4:148867400-148882000	Weak transcription	HSMMtube	muscle
46	chr4:148868000-148876800	Weak transcription	NHEK	skin
47	chr4:148868200-148872400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:148868200-148878200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr4:148868200-148902600	Weak transcription	NH-A	brain
50	chr4:148868400-148873400	Strong transcription	Fetal Muscle Trunk	muscle

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