Variant report

Variant	rs9648483
Chromosome Location	chr7:39727862-39727863
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:39723283..39725435-chr7:39727516..39730400,2	MCF-7	breast:
2	chr7:39661404..39663086-chr7:39725958..39728030,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006451	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10253933	0.83[ASN][1000 genomes]
rs10267545	0.83[ASN][1000 genomes]
rs10486803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486805	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12668144	1.00[ASN][1000 genomes]
rs12669963	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12701754	0.96[ASN][1000 genomes]
rs12701755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701756	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12701757	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13247563	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17417049	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17417084	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34063025	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35774126	1.00[ASN][1000 genomes]
rs35943406	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3779200	1.00[ASN][1000 genomes]
rs6462940	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968684	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976944	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977082	1.00[ASN][1000 genomes]
rs7778955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7779169	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7792940	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7797693	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv887971	chr7:39662268-39745775	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv887972	chr7:39666267-39733688	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39700000-39728200	Weak transcription	Liver	Liver
2	chr7:39701800-39739400	Weak transcription	Esophagus	oesophagus
3	chr7:39707200-39730000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr7:39712800-39728400	Weak transcription	Pancreas	Pancrea
5	chr7:39714000-39736800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr7:39715000-39736600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:39715200-39749400	Weak transcription	Aorta	Aorta
8	chr7:39716800-39728400	Weak transcription	Primary B cells from cord blood	blood
9	chr7:39716800-39729200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr7:39716800-39735600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:39718200-39739800	Weak transcription	Spleen	Spleen
12	chr7:39719800-39728600	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr7:39720000-39728600	Weak transcription	HepG2	liver
14	chr7:39720200-39728400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:39721200-39730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:39721200-39738200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:39721400-39730000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr7:39721400-39735800	Weak transcription	K562	blood
19	chr7:39721800-39736400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr7:39721800-39736600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:39722000-39737600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:39722800-39728400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr7:39722800-39728600	Weak transcription	Lung	lung
24	chr7:39722800-39730000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:39722800-39738400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:39723000-39728400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:39723000-39728600	Weak transcription	Gastric	stomach
28	chr7:39723000-39729200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:39723000-39731200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr7:39723200-39728200	Weak transcription	Ovary	ovary
31	chr7:39723200-39730000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr7:39723200-39730000	Weak transcription	Psoas Muscle	Psoas
33	chr7:39723200-39736000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr7:39723400-39728200	Weak transcription	Dnd41	blood
35	chr7:39723400-39729800	Weak transcription	Brain Germinal Matrix	brain
36	chr7:39723400-39736800	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:39723600-39729800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:39723600-39730200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr7:39723600-39742800	Weak transcription	Brain Angular Gyrus	brain
40	chr7:39723800-39728200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:39723800-39728200	Weak transcription	HMEC	breast
42	chr7:39723800-39728400	Weak transcription	A549	lung
43	chr7:39723800-39729800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr7:39723800-39730000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:39723800-39730000	Weak transcription	Fetal Kidney	kidney
46	chr7:39723800-39736200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr7:39723800-39737000	Weak transcription	Brain Anterior Caudate	brain
48	chr7:39723800-39743000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr7:39724000-39728400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr7:39724000-39728400	Weak transcription	Hela-S3	cervix

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