Variant report

Variant	rs60409279
Chromosome Location	chr2:96872400-96872401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:96872146-96873938	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:96856180..96863246-chr2:96870668..96875373,10	MCF-7	breast:
2	chr2:96808076..96814305-chr2:96871431..96875215,8	MCF-7	breast:
3	chr2:96872287..96875218-chr2:97169522..97172410,2	MCF-7	breast:
4	chr2:96868913..96876440-chr2:96928017..96934530,23	K562	blood:
5	chr2:96870309..96876262-chr2:96928720..96933891,16	MCF-7	breast:
6	chr2:96871739..96877156-chr2:96928674..96935050,17	K562	blood:
7	chr2:96871572..96876906-chr2:96928916..96935631,15	MCF-7	breast:
8	chr2:96803078..96804827-chr2:96870738..96872639,2	K562	blood:

No data

Variant related genes	Relation type
STARD7-AS1	TF binding region
ENSG00000135956	Chromatin interaction
ENSG00000158050	Chromatin interaction
ENSG00000163121	Chromatin interaction
ENSG00000188886	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000228873	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12617019	0.81[EUR][1000 genomes]
rs12618133	0.80[EUR][1000 genomes]
rs17119615	1.00[AFR][1000 genomes]
rs3852673	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4371393	0.81[EUR][1000 genomes]
rs4592891	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4826	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56088823	0.91[AFR][1000 genomes]
rs57476471	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59082429	0.95[ASN][1000 genomes]
rs59664047	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61624166	0.91[AFR][1000 genomes]
rs62152966	1.00[AFR][1000 genomes]
rs62152972	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153011	1.00[ASN][1000 genomes]
rs62153014	0.81[EUR][1000 genomes]
rs62153018	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153020	0.80[EUR][1000 genomes]
rs62153022	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153029	0.80[EUR][1000 genomes]
rs6576968	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6756208	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72825854	1.00[ASN][1000 genomes]
rs72825856	1.00[ASN][1000 genomes]
rs72825864	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72825877	0.80[EUR][1000 genomes]
rs73958180	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579709	0.81[EUR][1000 genomes]
rs7580178	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs997547	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997548	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3435047	chr2:96836850-96890437	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
9	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60409279	AC008268.2	cis	Artery Tibial	GTEx

Chromatin state (count:135 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96849600-96872600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:96859000-96873200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:96861400-96872800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:96861400-96872800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:96864200-96872600	Enhancers	Brain Substantia Nigra	brain
6	chr2:96866200-96872800	Enhancers	Adipose Nuclei	Adipose
7	chr2:96866400-96872800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:96867000-96872600	Enhancers	Fetal Muscle Leg	muscle
9	chr2:96867000-96873000	Enhancers	Small Intestine	intestine
10	chr2:96867600-96872800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr2:96867800-96873000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr2:96868800-96872800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:96869400-96872800	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:96869600-96872600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:96869600-96872800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr2:96869600-96872800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr2:96869600-96872800	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr2:96869800-96872800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:96869800-96873000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr2:96870000-96872800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:96870000-96873000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr2:96870000-96873200	Weak transcription	Gastric	stomach
23	chr2:96870000-96875400	Active TSS	Psoas Muscle	Psoas
24	chr2:96870200-96873000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:96870200-96873000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:96870400-96872400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:96870400-96872800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:96870400-96872800	Weak transcription	Lung	lung
29	chr2:96870400-96873000	Weak transcription	Esophagus	oesophagus
30	chr2:96870400-96873000	Weak transcription	Pancreas	Pancrea
31	chr2:96870400-96873400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:96870400-96875400	Active TSS	Right Ventricle	heart
33	chr2:96870600-96872400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:96870800-96872600	Enhancers	Fetal Brain Male	brain
35	chr2:96870800-96872800	Genic enhancers	Fetal Thymus	thymus
36	chr2:96870800-96872800	Flanking Active TSS	HepG2	liver
37	chr2:96871000-96872400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:96871000-96872400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:96871000-96872600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:96871000-96872800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr2:96871000-96872800	Enhancers	Colonic Mucosa	Colon
42	chr2:96871000-96873200	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr2:96871000-96874400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:96871200-96872800	Enhancers	Thymus	Thymus
45	chr2:96871400-96872600	Enhancers	Liver	Liver
46	chr2:96871400-96872600	Enhancers	Rectal Smooth Muscle	rectum
47	chr2:96871400-96872800	Enhancers	Colon Smooth Muscle	Colon
48	chr2:96871400-96875200	Active TSS	Left Ventricle	heart
49	chr2:96871400-96875400	Active TSS	NHLF	lung
50	chr2:96871600-96872400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell

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