Variant report

Variant	rs7612579
Chromosome Location	chr3:194866083-194866084
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:194866003-194866304	MCF-7	breast:	n/a	n/a
2	POLR2A	chr3:194866038-194866395	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194825282..194827537-chr3:194865128..194866939,2	K562	blood:
2	chr3:194864066..194866570-chr3:194866869..194868881,2	K562	blood:
3	chr3:194865591..194868396-chr3:194874419..194877392,2	K562	blood:

Variant related genes	Relation type
XXYLT1-AS2	TF binding region
ENSG00000230266	Chromatin interaction
ENSG00000244314	Chromatin interaction
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11917068	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1552893	0.82[AMR][1000 genomes]
rs2172695	0.85[AMR][1000 genomes]
rs2279630	0.85[AMR][1000 genomes]
rs28573813	0.87[AMR][1000 genomes]
rs4266129	0.86[AMR][1000 genomes]
rs4300953	0.83[AMR][1000 genomes]
rs4645095	0.81[AMR][1000 genomes]
rs4677663	0.83[AMR][1000 genomes]
rs4677812	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58370605	0.81[AMR][1000 genomes]
rs6794540	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7639698	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7646496	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs903310	0.86[AMR][1000 genomes]
rs950257	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	esv3355933	chr3:194865955-194866488	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194841000-194872800	Weak transcription	HSMMtube	muscle
2	chr3:194841400-194868800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:194846600-194868400	Weak transcription	HepG2	liver
4	chr3:194847200-194868200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:194852400-194868400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:194854600-194866200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:194854600-194868400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:194854600-194868600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:194854600-194871000	Weak transcription	Fetal Brain Female	brain
10	chr3:194854800-194868400	Weak transcription	NHLF	lung
11	chr3:194855400-194868800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:194858600-194866800	Weak transcription	Gastric	stomach
13	chr3:194860400-194868200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:194860400-194868400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:194860600-194868400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:194860800-194866800	Weak transcription	Right Atrium	heart
17	chr3:194860800-194870200	Weak transcription	Right Ventricle	heart
18	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
19	chr3:194861200-194872600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:194861600-194870800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:194861800-194868200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:194861800-194868200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:194861800-194868200	Weak transcription	Adipose Nuclei	Adipose
24	chr3:194861800-194869000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:194861800-194870800	Weak transcription	Aorta	Aorta
26	chr3:194861800-194871000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr3:194861800-194871200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:194861800-194872800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr3:194861800-194875000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:194862200-194866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr3:194862200-194867200	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:194862200-194868600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr3:194862200-194869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr3:194862400-194870600	Weak transcription	Osteobl	bone
35	chr3:194862400-194897800	Weak transcription	Dnd41	blood
36	chr3:194862600-194869200	Weak transcription	Fetal Intestine Small	intestine
37	chr3:194862800-194866800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:194862800-194866800	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:194862800-194868400	Weak transcription	Primary T cells from cord blood	blood
40	chr3:194863000-194868400	Weak transcription	Esophagus	oesophagus
41	chr3:194863000-194869200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:194863000-194869400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:194863200-194866400	Weak transcription	HUVEC	blood vessel
44	chr3:194863200-194867800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:194863600-194868400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr3:194863800-194870200	Weak transcription	Ovary	ovary
47	chr3:194864000-194866800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:194864000-194867600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr3:194864200-194868200	Enhancers	Primary B cells from peripheral blood	blood
50	chr3:194864400-194870800	Weak transcription	Brain Angular Gyrus	brain

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