Variant report

Variant	rs10464604
Chromosome Location	chr7:99034076-99034077
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99033904-99034165	K562	blood:	n/a	n/a
2	POLR2A	chr7:99033396-99034181	K562	blood:	n/a	n/a
3	POLR2A	chr7:99033711-99034802	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99001484..99003635-chr7:99032738..99035703,2	K562	blood:
2	chr7:99032776..99034323-chr7:99036979..99038480,2	MCF-7	breast:
3	chr7:99004207..99009187-chr7:99032699..99039268,13	MCF-7	breast:
4	chr7:99027922..99030424-chr7:99032965..99035110,3	K562	blood:
5	chr7:99010009..99013201-chr7:99032916..99037248,5	MCF-7	breast:
6	chr7:99030944..99035080-chr7:99035226..99039444,6	MCF-7	breast:
7	chr7:98970391..98972681-chr7:99033800..99036309,2	K562	blood:

No data

Variant related genes	Relation type
PTCD1	TF binding region
CPSF4	TF binding region
ENSG00000239133	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1002172	0.84[EUR][1000 genomes]
rs1004387	0.83[EUR][1000 genomes]
rs10225314	0.84[EUR][1000 genomes]
rs10240199	0.82[ASN][1000 genomes]
rs10244158	0.82[ASN][1000 genomes]
rs10265385	0.84[ASN][1000 genomes]
rs10271049	0.86[ASN][1000 genomes]
rs1043466	0.81[ASN][1000 genomes]
rs11539770	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538826	0.99[ASN][1000 genomes]
rs13227795	0.81[ASN][1000 genomes]
rs13240600	0.81[ASN][1000 genomes]
rs13437771	0.81[ASN][1000 genomes]
rs17161652	0.92[EUR][1000 genomes]
rs17161677	1.00[EUR][1000 genomes]
rs17161698	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17161766	0.92[EUR][1000 genomes]
rs17161768	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161769	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17161771	0.84[EUR][1000 genomes]
rs17161772	0.84[EUR][1000 genomes]
rs17161774	0.92[EUR][1000 genomes]
rs17161780	0.92[EUR][1000 genomes]
rs17161783	0.92[EUR][1000 genomes]
rs1980307	0.81[ASN][1000 genomes]
rs1985453	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2057906	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2107705	1.00[EUR][1000 genomes]
rs2240384	0.86[ASN][1000 genomes]
rs2240385	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269985	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2280600	0.81[ASN][1000 genomes]
rs2280601	0.81[ASN][1000 genomes]
rs2404322	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28457808	0.81[ASN][1000 genomes]
rs3764815	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3779354	0.82[ASN][1000 genomes]
rs3800960	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3823812	0.92[EUR][1000 genomes]
rs45492098	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45540134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45622743	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4646446	0.92[EUR][1000 genomes]
rs4646447	0.92[EUR][1000 genomes]
rs4646449	0.92[EUR][1000 genomes]
rs4646453	0.92[EUR][1000 genomes]
rs4646456	0.92[EUR][1000 genomes]
rs58024720	0.84[EUR][1000 genomes]
rs58222677	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58421977	1.00[EUR][1000 genomes]
rs59986060	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60301933	0.87[ASN][1000 genomes]
rs60865030	0.92[EUR][1000 genomes]
rs61159815	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61337492	0.92[EUR][1000 genomes]
rs61402640	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61543997	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6962772	0.82[ASN][1000 genomes]
rs72494451	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72494452	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73709637	1.00[EUR][1000 genomes]
rs73709641	1.00[EUR][1000 genomes]
rs7794682	0.86[ASN][1000 genomes]
rs7794705	0.83[ASN][1000 genomes]
rs883403	0.83[ASN][1000 genomes]
rs917154	0.81[ASN][1000 genomes]
rs940336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99011400-99035000	Weak transcription	Fetal Brain Male	brain
3	chr7:99015600-99035200	Weak transcription	Fetal Kidney	kidney
4	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
6	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:99018200-99035200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr7:99021400-99034400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:99021600-99035200	Weak transcription	HMEC	breast
13	chr7:99022200-99035400	Weak transcription	NH-A	brain
14	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
15	chr7:99025600-99034400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:99025600-99034800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:99025600-99034800	Strong transcription	Fetal Muscle Leg	muscle
18	chr7:99025600-99035200	Strong transcription	Fetal Stomach	stomach
19	chr7:99026200-99034400	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr7:99026200-99034600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:99026800-99034200	Strong transcription	Primary T cells from cord blood	blood
22	chr7:99027200-99035400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr7:99027200-99035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:99028000-99035600	Weak transcription	Primary B cells from cord blood	blood
25	chr7:99028200-99034200	Weak transcription	GM12878-XiMat	blood
26	chr7:99030600-99035200	Weak transcription	HSMM	muscle
27	chr7:99031000-99034400	Weak transcription	Esophagus	oesophagus
28	chr7:99031000-99035400	Weak transcription	Fetal Lung	lung
29	chr7:99031200-99034800	Weak transcription	HepG2	liver
30	chr7:99031400-99035400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr7:99031400-99035400	Weak transcription	Brain Anterior Caudate	brain
32	chr7:99031600-99035200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr7:99032000-99034400	Strong transcription	NHLF	lung
34	chr7:99032400-99035200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:99032400-99035200	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:99032600-99035200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr7:99032600-99035200	Weak transcription	NHDF-Ad	bronchial
38	chr7:99032600-99035400	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:99032600-99035400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr7:99032800-99034400	Weak transcription	Hela-S3	cervix
41	chr7:99032800-99035000	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr7:99032800-99035200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:99032800-99035200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr7:99032800-99035200	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr7:99032800-99035200	Weak transcription	Brain Angular Gyrus	brain
46	chr7:99032800-99035200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr7:99032800-99035200	Weak transcription	Fetal Brain Female	brain
48	chr7:99032800-99035200	Weak transcription	Fetal Intestine Large	intestine
49	chr7:99032800-99035200	Weak transcription	Fetal Thymus	thymus
50	chr7:99032800-99035200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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