Variant report

Variant	rs6414350
Chromosome Location	chr3:142316660-142316661
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
2	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
3	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
4	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
5	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
6	chr3:142314277..142316663-chr3:142382049..142384101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242390	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000175054	Chromatin interaction
ENSG00000144935	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	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129393	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13065075	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067795	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13069307	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075471	0.83[EUR][1000 genomes]
rs13085998	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13093869	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098343	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357529	0.81[EUR][1000 genomes]
rs1357530	0.83[EUR][1000 genomes]
rs1916639	0.83[EUR][1000 genomes]
rs1983434	0.83[EUR][1000 genomes]
rs1983435	0.83[EUR][1000 genomes]
rs2030613	0.83[EUR][1000 genomes]
rs2049325	0.83[EUR][1000 genomes]
rs2049326	0.83[EUR][1000 genomes]
rs2140432	0.83[EUR][1000 genomes]
rs2177396	0.83[EUR][1000 genomes]
rs2227928	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227930	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354860	0.84[EUR][1000 genomes]
rs28617475	0.80[ASN][1000 genomes]
rs4413348	0.83[EUR][1000 genomes]
rs6440086	0.85[ASN][1000 genomes]
rs6440087	0.90[ASN][1000 genomes]
rs6440088	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440089	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440090	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440091	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440092	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440093	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440094	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440098	0.82[EUR][1000 genomes]
rs6440099	0.83[EUR][1000 genomes]
rs6768093	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770155	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775813	0.83[EUR][1000 genomes]
rs6782400	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783203	0.83[EUR][1000 genomes]
rs6784089	0.83[EUR][1000 genomes]
rs6791816	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792259	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799752	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7428496	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7610557	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615316	0.83[EUR][1000 genomes]
rs7623524	0.86[ASN][1000 genomes]
rs7630130	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631313	0.82[EUR][1000 genomes]
rs7634158	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635146	0.83[EUR][1000 genomes]
rs7641330	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.83[EUR][1000 genomes]
rs7647573	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651071	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651542	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683085	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808914	0.90[ASN][1000 genomes]
rs9808943	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9820353	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9824176	0.82[EUR][1000 genomes]
rs9824893	0.83[EUR][1000 genomes]
rs9825207	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9846960	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9855919	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9866958	0.82[EUR][1000 genomes]
rs9869842	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876254	0.87[ASN][1000 genomes]
rs9879995	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882763	0.83[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:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142314200-142317800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:142314400-142316800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:142314400-142317200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:142314400-142317400	Active TSS	Colonic Mucosa	Colon
5	chr3:142314400-142317400	Active TSS	Fetal Kidney	kidney
6	chr3:142314400-142317600	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:142314400-142317800	Active TSS	Duodenum Mucosa	Duodenum
8	chr3:142314600-142317600	Active TSS	Stomach Mucosa	stomach
9	chr3:142314800-142316800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr3:142314800-142316800	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr3:142315600-142317000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:142315600-142317200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:142315600-142317400	Flanking Active TSS	Dnd41	blood
14	chr3:142315600-142319200	Weak transcription	Gastric	stomach
15	chr3:142315800-142316800	Weak transcription	Pancreas	Pancrea
16	chr3:142315800-142318000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr3:142315800-142320400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:142315800-142324400	Weak transcription	Lung	lung
19	chr3:142316000-142316800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:142316000-142317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr3:142316000-142317000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:142316000-142317200	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:142316000-142317200	Active TSS	Fetal Stomach	stomach
24	chr3:142316000-142317200	Flanking Active TSS	NHEK	skin
25	chr3:142316000-142317400	Enhancers	Fetal Thymus	thymus
26	chr3:142316000-142319800	Weak transcription	NH-A	brain
27	chr3:142316000-142321000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:142316000-142321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:142316200-142316800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:142316200-142316800	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr3:142316200-142316800	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:142316200-142316800	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr3:142316200-142317000	Enhancers	H1 Cell Line	embryonic stem cell
34	chr3:142316200-142317000	Flanking Active TSS	A549	lung
35	chr3:142316200-142317200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:142316200-142317200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:142316200-142317200	Enhancers	Thymus	Thymus
38	chr3:142316200-142317400	Enhancers	Liver	Liver
39	chr3:142316200-142317400	Enhancers	Hela-S3	cervix
40	chr3:142316200-142318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:142316200-142331000	Weak transcription	Small Intestine	intestine
42	chr3:142316400-142316800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:142316400-142317000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:142316400-142317000	Flanking Active TSS	HepG2	liver
45	chr3:142316400-142317200	Flanking Active TSS	K562	blood
46	chr3:142316400-142317400	Enhancers	Esophagus	oesophagus
47	chr3:142316400-142317400	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr3:142316600-142316800	Active TSS	Fetal Intestine Large	intestine
49	chr3:142316600-142317000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
50	chr3:142316600-142317000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet

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