Variant report

Variant	rs998647
Chromosome Location	chr3:112981798-112981799
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	chr3:112859990..112861928-chr3:112980723..112983523,2	MCF-7	breast:
2	chr3:112981093..112982647-chr3:112988847..112990672,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1499898	0.95[ASN][1000 genomes]
rs16845106	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16860709	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16860720	0.95[ASN][1000 genomes]
rs16860770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17255950	1.00[AFR][1000 genomes]
rs17256551	1.00[AFR][1000 genomes]
rs17256752	1.00[AFR][1000 genomes]
rs17320040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17320242	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17322613	1.00[AFR][1000 genomes]
rs2291412	1.00[AFR][1000 genomes]
rs2399476	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34600669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41271353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56772417	1.00[AFR][1000 genomes]
rs57104308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57115529	1.00[AFR][1000 genomes]
rs57164268	1.00[AFR][1000 genomes]
rs58905600	1.00[AFR][1000 genomes]
rs58988763	1.00[AFR][1000 genomes]
rs59493419	1.00[AFR][1000 genomes]
rs59590258	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59742486	1.00[AFR][1000 genomes]
rs60070011	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60582065	1.00[AFR][1000 genomes]
rs60697865	1.00[AFR][1000 genomes]
rs60940543	1.00[AFR][1000 genomes]
rs61035513	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61594119	1.00[AFR][1000 genomes]
rs735	1.00[AFR][1000 genomes]
rs9820139	1.00[ASN][1000 genomes]
rs9832953	0.98[ASN][1000 genomes]
rs9849714	0.95[ASN][1000 genomes]
rs9855011	0.95[ASN][1000 genomes]
rs9872998	1.00[ASN][1000 genomes]
rs9878424	1.00[ASN][1000 genomes]
rs999365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 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	chr3:112961600-112983000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:112969000-112995200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:112969800-112991800	Weak transcription	Right Ventricle	heart
4	chr3:112969800-112994200	Weak transcription	Spleen	Spleen
5	chr3:112971800-112986400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:112972400-112986400	Weak transcription	Fetal Intestine Small	intestine
7	chr3:112973400-112981800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:112973400-112982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:112973400-112987600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:112973600-112982000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:112973600-112983600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr3:112973600-112993000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:112973600-112997200	Weak transcription	Colonic Mucosa	Colon
14	chr3:112973800-112981800	Weak transcription	Psoas Muscle	Psoas
15	chr3:112973800-112983400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:112974200-112981800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:112974200-112994600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:112974600-112982200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:112974800-112981800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:112974800-112983200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:112976400-112988600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:112976800-112982000	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:112977600-112981800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:112977800-112982200	Enhancers	Adipose Nuclei	Adipose
25	chr3:112978600-112983800	Weak transcription	Brain Angular Gyrus	brain
26	chr3:112978600-112991400	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:112978800-112984400	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr3:112979400-112984800	Genic enhancers	Fetal Stomach	stomach
29	chr3:112979600-112981800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:112979600-112985600	Enhancers	Fetal Brain Female	brain
31	chr3:112980000-112981800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:112980000-112982000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:112980600-112984000	Enhancers	HSMMtube	muscle
34	chr3:112980600-112984400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:112980800-112982000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:112980800-112982000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:112980800-112982000	Enhancers	Ovary	ovary
38	chr3:112981000-112982000	Enhancers	Esophagus	oesophagus
39	chr3:112981000-112982000	Genic enhancers	NHDF-Ad	bronchial
40	chr3:112981000-112982200	Enhancers	Pancreas	Pancrea
41	chr3:112981000-112982600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:112981000-112982600	Enhancers	NHEK	skin
43	chr3:112981000-112982800	Enhancers	HMEC	breast
44	chr3:112981000-112983000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:112981000-112984200	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:112981000-112984200	Enhancers	HSMM	muscle
47	chr3:112981000-112986600	Enhancers	Brain Substantia Nigra	brain
48	chr3:112981200-112982000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:112981200-112982000	Enhancers	Brain Hippocampus Middle	brain
50	chr3:112981200-112982200	Genic enhancers	Fetal Muscle Trunk	muscle

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