Variant report

Variant	rs10225647
Chromosome Location	chr7:121007563-121007564
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	CTCF	chr7:121006549-121008081	A549	lung:	n/a	chr7:121007076-121007097 chr7:121007074-121007092 chr7:121007077-121007090
2	SMC3	chr7:121006348-121007680	SK-N-SH	brain:	n/a	chr7:121007076-121007090
3	RAD21	chr7:121005769-121008532	SK-N-SH	brain:	n/a	chr7:121007079-121007088 chr7:121007080-121007092 chr7:121007075-121007094 chr7:121007078-121007091
4	POLR2A	chr7:121006747-121007909	GM12878	blood:	n/a	n/a
5	POLR2A	chr7:121007524-121007721	MCF10A-Er-Src	breast:	n/a	n/a
6	SMC3	chr7:121006765-121007679	GM12878	blood:	n/a	chr7:121007076-121007090

No.	Distal block	Cell Line	Cell type
1	chr7:121006747..121007563-chr7:121149688..121150676,2	K562	blood:
2	chr7:121006580..121008366-chr7:121155081..121156610,2	K562	blood:
3	chr7:121007055..121007746-chr7:121036256..121036915,3	K562	blood:
4	chr7:121006680..121008574-chr7:121018807..121020891,2	K562	blood:
5	chr7:121007156..121009116-chr7:121011586..121013929,2	K562	blood:
6	chr7:121007069..121007588-chr7:121634575..121635222,2	K562	blood:
7	chr7:121006586..121008267-chr7:121187006..121188236,8	MCF-7	breast:
8	chr17:57920914..57923134-chr7:121006073..121007624,2	MCF-7	breast:
9	chr7:121006292..121008390-chr7:121186488..121188741,23	K562	blood:
10	chr7:121007095..121012773-chr7:121032215..121038175,10	MCF-7	breast:
11	chr7:121006823..121007565-chr7:121187243..121187877,3	MCF-7	breast:
12	chr7:121005362..121009236-chr7:121034882..121036635,4	MCF-7	breast:

Variant related genes	Relation type
FAM3C	TF binding region
ENSG00000196937	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10232028	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10237944	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs10248910	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10270194	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs10274424	1.00[AMR][1000 genomes]
rs12111905	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12535821	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12536771	0.85[YRI][hapmap]
rs13438018	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs17143353	0.84[ASW][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17143357	0.84[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28635533	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2896303	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56835233	1.00[AMR][1000 genomes]
rs57412322	1.00[AMR][1000 genomes]
rs59723881	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6943177	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6944198	1.00[AMR][1000 genomes]
rs6944409	0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs6960006	1.00[AMR][1000 genomes]
rs6975632	0.85[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025430	chr7:120638930-121179289	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1034353	chr7:120818382-121040576	Enhancers Bivalent Enhancer Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	19 gene(s)	inside rSNPs	diseases
3	nsv1026322	chr7:120841937-121188037	Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv539102	chr7:120841937-121188037	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2755350	chr7:120848049-121119049	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1032054	chr7:120926379-121432971	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv539103	chr7:120926379-121432971	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS 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 target site	20 gene(s)	inside rSNPs	diseases
8	esv1799806	chr7:120997195-121008204	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120970600-121016800	Weak transcription	Gastric	stomach
2	chr7:120970600-121025400	Weak transcription	Spleen	Spleen
3	chr7:120978800-121017400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr7:120979800-121019400	Weak transcription	Thymus	Thymus
5	chr7:120979800-121034800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:120980800-121019600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:120981000-121015200	Weak transcription	Pancreas	Pancrea
8	chr7:120983000-121009600	Weak transcription	Hela-S3	cervix
9	chr7:120984000-121017600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:120984200-121009800	Weak transcription	Fetal Brain Male	brain
11	chr7:120984200-121035000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr7:120984800-121009600	Weak transcription	A549	lung
13	chr7:120985000-121009600	Weak transcription	Small Intestine	intestine
14	chr7:120985200-121013000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:120986200-121029600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:120986400-121026000	Weak transcription	Colonic Mucosa	Colon
17	chr7:120986400-121026000	Weak transcription	Psoas Muscle	Psoas
18	chr7:120989200-121015400	Weak transcription	Brain Anterior Caudate	brain
19	chr7:120989600-121016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr7:120990400-121008600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:120990600-121008800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr7:120990600-121009000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr7:120990600-121009000	Strong transcription	HSMM	muscle
24	chr7:120991000-121012600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr7:120991800-121010800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr7:120993000-121025600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr7:120993600-121015400	Weak transcription	Esophagus	oesophagus
28	chr7:120994600-121011600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr7:120994800-121009400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr7:120994800-121015600	Weak transcription	Lung	lung
31	chr7:120995600-121012600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr7:120995600-121026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr7:120995800-121016000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr7:120996000-121015400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr7:120996400-121018400	Strong transcription	HMEC	breast
36	chr7:120997000-121009400	Weak transcription	Fetal Lung	lung
37	chr7:120998000-121009400	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:120998000-121017400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr7:121000000-121007600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr7:121000000-121007800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:121000000-121024200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr7:121000400-121007800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr7:121000800-121012000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr7:121000800-121029600	Weak transcription	Brain Angular Gyrus	brain
45	chr7:121001000-121009400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr7:121001000-121009600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:121001000-121010600	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr7:121001000-121026000	Weak transcription	Aorta	Aorta
49	chr7:121001200-121015600	Weak transcription	Placenta	Placenta
50	chr7:121001400-121012800	Weak transcription	Fetal Kidney	kidney

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