Variant report

Variant	rs2364921
Chromosome Location	chr3:158522463-158522464
allele	A/G
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	STAT3	chr3:158522353-158522463	MCF10A-Er-Src	breast:	n/a	chr3:158522404-158522411
2	FOS	chr3:158522288-158522598	MCF10A-Er-Src	breast:	n/a	chr3:158522464-158522474
3	MAFK	chr3:158522016-158522562	K562	blood:	n/a	n/a
4	FOS	chr3:158522355-158522555	MCF10A-Er-Src	breast:	n/a	chr3:158522464-158522474
5	FOS	chr3:158522306-158522626	MCF10A-Er-Src	breast:	n/a	chr3:158522464-158522474
6	CUX1	chr3:158522385-158522465	K562	blood:	n/a	n/a
7	FOS	chr3:158522338-158522566	HUVEC	blood vessel:	n/a	chr3:158522464-158522474

No.	Distal block	Cell Line	Cell type
1	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:
2	chr3:158520933..158523122-chr3:158539093..158541854,2	K562	blood:
3	chr3:158519555..158521596-chr3:158521665..158523312,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272247	TF binding region
MFSD1	TF binding region
ENSG00000272247	Chromatin interaction
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10936160	0.85[ASN][1000 genomes]
rs12493280	0.85[ASN][1000 genomes]
rs12638831	0.85[ASN][1000 genomes]
rs1381463	0.85[ASN][1000 genomes]
rs2244996	0.95[ASN][1000 genomes]
rs2713736	0.95[ASN][1000 genomes]
rs6802315	0.83[EUR][1000 genomes]
rs6802844	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7429205	0.86[ASN][1000 genomes]
rs7615751	0.81[AFR][1000 genomes]
rs9822005	0.81[AFR][1000 genomes]
rs9861042	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS 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 miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2364921	RP11-379F4.9	cis	Thyroid	GTEx
rs2364921	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158527400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
3	chr3:158520600-158522600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:158520600-158522800	Enhancers	HUVEC	blood vessel
5	chr3:158520600-158524200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:158520600-158525600	Weak transcription	Fetal Kidney	kidney
7	chr3:158520600-158525600	Weak transcription	Gastric	stomach
8	chr3:158520600-158525600	Weak transcription	Left Ventricle	heart
9	chr3:158520600-158525600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:158520600-158525600	Weak transcription	Spleen	Spleen
11	chr3:158520600-158525800	Weak transcription	Pancreas	Pancrea
12	chr3:158520600-158526200	Weak transcription	Esophagus	oesophagus
13	chr3:158520600-158526400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:158520600-158527000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:158520600-158543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:158520800-158522800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr3:158520800-158522800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:158520800-158523400	Weak transcription	Fetal Stomach	stomach
19	chr3:158520800-158525400	Weak transcription	Brain Angular Gyrus	brain
20	chr3:158520800-158525600	Weak transcription	Aorta	Aorta
21	chr3:158520800-158525600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:158520800-158525600	Weak transcription	Ovary	ovary
23	chr3:158520800-158525800	Weak transcription	Colonic Mucosa	Colon
24	chr3:158520800-158526400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:158520800-158526400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:158521000-158526400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:158521000-158527400	Weak transcription	Fetal Brain Male	brain
29	chr3:158521000-158527400	Weak transcription	Right Ventricle	heart
30	chr3:158521000-158543200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:158521200-158522600	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr3:158521200-158525400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:158521200-158525400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:158521200-158525400	Weak transcription	Fetal Intestine Large	intestine
35	chr3:158521200-158525400	Weak transcription	Lung	lung
36	chr3:158521200-158525400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:158521200-158525600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:158521200-158525600	Weak transcription	Brain Substantia Nigra	brain
39	chr3:158521200-158525600	Weak transcription	Fetal Brain Female	brain
40	chr3:158521200-158525600	Weak transcription	Fetal Intestine Small	intestine
41	chr3:158521200-158525600	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:158521200-158526200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:158521200-158526200	Weak transcription	HMEC	breast
44	chr3:158521200-158526400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:158521200-158526400	Weak transcription	Thymus	Thymus
46	chr3:158521200-158526400	Weak transcription	NHEK	skin
47	chr3:158521200-158526600	Weak transcription	HSMMtube	muscle
48	chr3:158521200-158527200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:158521200-158527400	Weak transcription	Psoas Muscle	Psoas
50	chr3:158521200-158527600	Weak transcription	Brain Germinal Matrix	brain

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