Variant report

Variant	rs7797354
Chromosome Location	chr7:97488733-97488734
allele	C/T
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	chr7:97480607-97497455	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:97481488..97486650-chr7:97486817..97491260,8	K562	blood:
2	chr7:97488155..97489772-chr7:97499944..97501920,2	MCF-7	breast:

Variant related genes	Relation type
ASNS	TF binding region
ENSG00000070669	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10253639	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261245	0.81[AMR][1000 genomes]
rs10261265	0.81[AMR][1000 genomes]
rs2074891	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2237287	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237289	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757675	0.93[ASN][1000 genomes]
rs7792744	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv428178	chr7:97402756-97648029	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS 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	20 gene(s)	inside rSNPs	diseases
3	esv2758124	chr7:97476284-97648029	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759546	chr7:97476284-97648029	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7797354	TRIM4	cis	parietal	SCAN
rs7797354	AGFG2	cis	parietal	SCAN
rs7797354	ASNS	cis	parietal	SCAN
rs7797354	PLOD3	cis	parietal	SCAN
rs7797354	ZAN	cis	parietal	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97475000-97492800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:97477600-97500600	Weak transcription	Thymus	Thymus
3	chr7:97479000-97501000	Weak transcription	Fetal Intestine Large	intestine
4	chr7:97479200-97500800	Weak transcription	Right Ventricle	heart
5	chr7:97479400-97501000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:97479400-97501000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr7:97479600-97501000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr7:97479800-97500200	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr7:97480000-97491800	Weak transcription	Stomach Mucosa	stomach
10	chr7:97480200-97500600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr7:97480600-97488800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:97480600-97489600	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr7:97480600-97498200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:97480600-97498200	Strong transcription	K562	blood
15	chr7:97480600-97498600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:97480800-97488800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:97480800-97488800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:97480800-97488800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:97480800-97490000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:97480800-97490600	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr7:97480800-97491000	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr7:97480800-97491000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr7:97480800-97491600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:97480800-97498400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:97481000-97488800	Strong transcription	Primary T cells from cord blood	blood
26	chr7:97481000-97500600	Weak transcription	NHDF-Ad	bronchial
27	chr7:97481200-97488800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:97481200-97498000	Weak transcription	Fetal Brain Male	brain
29	chr7:97481400-97500600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr7:97481400-97500600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:97481400-97500600	Weak transcription	Colon Smooth Muscle	Colon
32	chr7:97481400-97501000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr7:97481800-97489600	Weak transcription	Fetal Thymus	thymus
34	chr7:97481800-97492600	Weak transcription	Esophagus	oesophagus
35	chr7:97481800-97500800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:97481800-97501000	Weak transcription	Fetal Intestine Small	intestine
37	chr7:97481800-97501000	Weak transcription	Gastric	stomach
38	chr7:97481800-97501000	Weak transcription	Pancreas	Pancrea
39	chr7:97481800-97501000	Weak transcription	Spleen	Spleen
40	chr7:97482000-97498200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:97482200-97497800	Weak transcription	HMEC	breast
42	chr7:97482800-97489200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr7:97482800-97500800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr7:97483400-97490200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:97483600-97500600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr7:97483600-97500800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr7:97483800-97500800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr7:97484000-97489200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:97484000-97500400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:97484200-97493600	Weak transcription	GM12878-XiMat	blood

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