Variant report

Variant	rs7428496
Chromosome Location	chr3:142320532-142320533
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142318139..142320851-chr3:142442948..142445184,2	K562	blood:
2	chr3:142317992..142321770-chr3:142321788..142324487,4	K562	blood:
3	chr3:142319541..142323718-chr3:142324179..142327610,6	MCF-7	breast:
4	chr3:142313049..142317204-chr3:142317936..142324155,9	MCF-7	breast:
5	chr3:142314594..142316783-chr3:142317618..142320716,5	K562	blood:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction
ENSG00000120756	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10935465	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1129393	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13065075	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13067795	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13069307	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085998	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13093869	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13098343	0.82[ASN][1000 genomes]
rs1357529	0.85[EUR][1000 genomes]
rs1357530	0.87[EUR][1000 genomes]
rs1916639	0.87[EUR][1000 genomes]
rs1983434	0.88[EUR][1000 genomes]
rs1983435	0.88[EUR][1000 genomes]
rs2030613	0.88[EUR][1000 genomes]
rs2049325	0.88[EUR][1000 genomes]
rs2049326	0.88[EUR][1000 genomes]
rs2140432	0.88[EUR][1000 genomes]
rs2177396	0.88[EUR][1000 genomes]
rs2227928	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2227930	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2354860	0.86[EUR][1000 genomes]
rs4413348	0.88[EUR][1000 genomes]
rs6414350	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440087	0.85[ASN][1000 genomes]
rs6440088	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6440089	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6440090	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440091	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440092	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440093	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440094	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440098	0.87[EUR][1000 genomes]
rs6440099	0.88[EUR][1000 genomes]
rs6768093	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6770155	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6775813	0.88[EUR][1000 genomes]
rs6782400	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6783203	0.88[EUR][1000 genomes]
rs6784089	0.88[EUR][1000 genomes]
rs6791816	0.82[ASN][1000 genomes]
rs6792259	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6799752	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6802734	0.83[EUR][1000 genomes]
rs6802774	0.83[EUR][1000 genomes]
rs7609842	0.81[EUR][1000 genomes]
rs7610557	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7615316	0.88[EUR][1000 genomes]
rs7623524	0.81[ASN][1000 genomes]
rs7630130	0.85[ASN][1000 genomes]
rs7631313	0.87[EUR][1000 genomes]
rs7634158	0.80[ASN][1000 genomes]
rs7635146	0.87[EUR][1000 genomes]
rs7641330	0.90[ASN][1000 genomes]
rs7646880	0.88[EUR][1000 genomes]
rs7647573	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651071	0.83[ASN][1000 genomes]
rs7651542	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683085	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9808914	0.85[ASN][1000 genomes]
rs9808943	0.85[ASN][1000 genomes]
rs9820353	0.85[ASN][1000 genomes]
rs9824176	0.86[EUR][1000 genomes]
rs9824893	0.88[EUR][1000 genomes]
rs9825207	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9846960	0.90[ASN][1000 genomes]
rs9855919	0.82[ASN][1000 genomes]
rs9866958	0.87[EUR][1000 genomes]
rs9869842	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9876254	0.82[ASN][1000 genomes]
rs9879995	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9882763	0.88[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	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142315800-142324400	Weak transcription	Lung	lung
2	chr3:142316000-142321000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:142316000-142321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:142316200-142331000	Weak transcription	Small Intestine	intestine
5	chr3:142317000-142321000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:142317000-142327600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:142317200-142321800	Weak transcription	Thymus	Thymus
8	chr3:142317200-142337600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:142317400-142321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:142317400-142321000	Weak transcription	Liver	Liver
11	chr3:142317400-142322200	Weak transcription	Dnd41	blood
12	chr3:142317400-142322800	Weak transcription	Hela-S3	cervix
13	chr3:142317400-142323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:142317400-142327400	Weak transcription	K562	blood
15	chr3:142317400-142337800	Weak transcription	HepG2	liver
16	chr3:142317600-142320600	Weak transcription	Stomach Mucosa	stomach
17	chr3:142319400-142321000	Weak transcription	Gastric	stomach
18	chr3:142319400-142330000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:142319600-142320600	Weak transcription	Colonic Mucosa	Colon
20	chr3:142319600-142320600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:142319600-142324200	Weak transcription	Pancreas	Pancrea
22	chr3:142320400-142320600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr3:142320400-142321000	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr3:142320400-142321200	Genic enhancers	Fetal Intestine Small	intestine
25	chr3:142320400-142324600	Enhancers	Fetal Intestine Large	intestine

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