Variant report

Variant	rs6748200
Chromosome Location	chr2:100080895-100080896
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	MAFK	chr2:100080656-100080903	HepG2	liver:	n/a	chr2:100080777-100080792
2	NFYA	chr2:100080791-100080974	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:100080735..100084657-chr2:100090928..100093443,3	K562	blood:
2	chr2:100079371..100082089-chr2:100106220..100108086,2	MCF-7	breast:
3	chr2:100072001..100074970-chr2:100080545..100083472,2	MCF-7	breast:

Variant related genes	Relation type
REV1	TF binding region
ENSG00000135945	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10496336	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11885942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11887935	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11893359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11896520	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12466114	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12474305	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12479064	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1823569	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1922624	1.00[JPT][hapmap]
rs2141907	0.84[EUR][1000 genomes]
rs2305352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2309618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28369945	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28382977	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3087403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792143	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4341989	0.95[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4851203	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851207	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4851210	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61436115	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62153852	0.83[EUR][1000 genomes]
rs62155769	0.82[AMR][1000 genomes]
rs62155807	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714650	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs737094	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6748200	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
3	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
4	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
5	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
6	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
7	chr2:100055800-100092600	Weak transcription	Gastric	stomach
8	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:100065400-100087400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:100067400-100081400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:100073400-100090000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:100074200-100084800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:100075200-100090400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
15	chr2:100076200-100098400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:100076400-100084800	Weak transcription	Esophagus	oesophagus
18	chr2:100076600-100085400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:100076600-100094800	Weak transcription	Spleen	Spleen
20	chr2:100076600-100104200	Weak transcription	NHLF	lung
21	chr2:100078200-100081200	ZNF genes & repeats	GM12878-XiMat	blood
22	chr2:100078400-100083200	Weak transcription	Fetal Heart	heart
23	chr2:100078400-100083400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:100078400-100084800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:100078600-100081600	Weak transcription	Thymus	Thymus
26	chr2:100078600-100084000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:100078600-100084800	Weak transcription	Colon Smooth Muscle	Colon
28	chr2:100078600-100085000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr2:100078600-100085200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:100078600-100085800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:100078600-100087400	Weak transcription	HMEC	breast
32	chr2:100078600-100087600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:100078600-100088600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:100078600-100088800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:100078600-100091000	Weak transcription	Aorta	Aorta
36	chr2:100078600-100091000	Weak transcription	Lung	lung
37	chr2:100078600-100092200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:100078600-100092600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:100078600-100096800	Weak transcription	NH-A	brain
40	chr2:100078800-100082800	Weak transcription	Psoas Muscle	Psoas
41	chr2:100078800-100084800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:100078800-100084800	Weak transcription	Brain Angular Gyrus	brain
43	chr2:100078800-100084800	Weak transcription	Brain Hippocampus Middle	brain
44	chr2:100078800-100084800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr2:100078800-100085000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:100078800-100085000	Weak transcription	Fetal Brain Male	brain
47	chr2:100078800-100085200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr2:100078800-100088800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:100078800-100089000	Weak transcription	Ovary	ovary
50	chr2:100078800-100090000	Weak transcription	HUVEC	blood vessel

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