Variant report

Variant	rs7994222
Chromosome Location	chr13:30497954-30497955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:30480230..30482244-chr13:30496884..30498942,2	MCF-7	breast:
2	chr13:30418186..30420449-chr13:30497353..30498942,2	MCF-7	breast:
3	chr13:30496337..30498664-chr6:26123575..26125211,2	MCF-7	breast:
4	chr13:30482306..30489173-chr13:30491895..30500288,16	MCF-7	breast:
5	chr13:30410273..30412330-chr13:30496949..30498652,2	MCF-7	breast:
6	chr13:30474561..30476361-chr13:30497151..30499609,2	MCF-7	breast:
7	chr13:30492675..30494704-chr13:30496918..30499167,3	MCF-7	breast:
8	chr13:30420595..30432624-chr13:30489594..30503683,39	MCF-7	breast:
9	chr13:30391873..30393700-chr13:30497127..30499566,2	MCF-7	breast:
10	chr13:30487024..30489829-chr13:30495820..30498491,2	K562	blood:
11	chr13:30420962..30426189-chr13:30489163..30500098,34	MCF-7	breast:
12	chr13:30494996..30500904-chr13:30681667..30688775,12	MCF-7	breast:
13	chr13:30497791..30500360-chr13:30674614..30679278,4	MCF-7	breast:
14	chr13:30475291..30479868-chr13:30496674..30499474,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180596	Chromatin interaction
ENSG00000122042	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000224511	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1093631	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1325368	0.86[ASN][1000 genomes]
rs17631642	0.86[ASN][1000 genomes]
rs17688104	0.83[CHB][hapmap];0.86[ASN][1000 genomes]
rs2388239	0.80[ASN][1000 genomes]
rs3843677	0.87[ASN][1000 genomes]
rs3843678	0.84[ASN][1000 genomes]
rs4318068	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4769779	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4769780	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4769781	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs585668	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs634413	0.85[CHD][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs646917	0.80[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7319246	0.83[ASN][1000 genomes]
rs7320271	0.83[ASN][1000 genomes]
rs7320355	0.83[ASN][1000 genomes]
rs7320728	0.83[ASN][1000 genomes]
rs7322038	0.82[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7339208	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74042894	0.88[ASN][1000 genomes]
rs7992473	0.86[CHB][hapmap];0.88[ASN][1000 genomes]
rs843883	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs912788	0.81[CHB][hapmap]
rs927731	0.86[ASN][1000 genomes]
rs927732	0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs927733	0.83[ASN][1000 genomes]
rs9314990	0.87[MEX][hapmap]
rs9314991	0.82[ASW][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs9506244	0.82[ASW][hapmap];0.81[LWK][hapmap];0.87[MEX][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs9508594	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7994222	MTIF3	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30491600-30501000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr13:30492400-30500600	Enhancers	HMEC	breast
3	chr13:30493600-30498600	Weak transcription	Gastric	stomach
4	chr13:30494200-30501400	Enhancers	Stomach Mucosa	stomach
5	chr13:30495600-30500400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr13:30496000-30500000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:30496000-30500200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:30496400-30498000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr13:30496400-30499600	Enhancers	Pancreas	Pancrea
10	chr13:30496400-30499800	Enhancers	Right Ventricle	heart
11	chr13:30496400-30500000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr13:30496400-30500200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr13:30496400-30500200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:30496400-30500200	Enhancers	Fetal Muscle Leg	muscle
15	chr13:30496400-30500200	Enhancers	NHLF	lung
16	chr13:30496400-30500400	Enhancers	Placenta	Placenta
17	chr13:30496400-30500600	Enhancers	NHDF-Ad	bronchial
18	chr13:30496600-30498200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr13:30496600-30499000	Flanking Active TSS	Osteobl	bone
20	chr13:30496600-30499800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:30496600-30500000	Enhancers	Fetal Stomach	stomach
22	chr13:30496600-30500800	Enhancers	Liver	Liver
23	chr13:30496800-30498400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr13:30496800-30499200	Enhancers	Thymus	Thymus
25	chr13:30496800-30499400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:30496800-30499600	Enhancers	Fetal Muscle Trunk	muscle
27	chr13:30496800-30499600	Enhancers	Left Ventricle	heart
28	chr13:30496800-30500200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:30496800-30500400	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr13:30496800-30500800	Enhancers	Brain Hippocampus Middle	brain
31	chr13:30496800-30501000	Enhancers	Fetal Intestine Small	intestine
32	chr13:30497000-30498000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr13:30497000-30498200	Enhancers	Brain Anterior Caudate	brain
34	chr13:30497000-30498200	Enhancers	Colon Smooth Muscle	Colon
35	chr13:30497000-30498600	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr13:30497000-30498800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:30497000-30498800	Enhancers	Adipose Nuclei	Adipose
38	chr13:30497000-30500000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr13:30497000-30500000	Enhancers	Fetal Intestine Large	intestine
40	chr13:30497000-30500000	Enhancers	Fetal Thymus	thymus
41	chr13:30497000-30500000	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr13:30497000-30500800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr13:30497000-30501000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr13:30497200-30498200	Enhancers	Rectal Smooth Muscle	rectum
45	chr13:30497200-30498200	Flanking Active TSS	A549	lung
46	chr13:30497200-30498400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr13:30497200-30498400	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr13:30497200-30498400	Enhancers	Fetal Kidney	kidney
49	chr13:30497200-30498800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
50	chr13:30497200-30499000	Enhancers	HUES64 Cell Line	embryonic stem cell

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