Variant report

Variant	rs28643391
Chromosome Location	chr4:3193199-3193200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3192746..3194310-chr4:3485907..3488354,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175920	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10006373	0.92[EUR][1000 genomes]
rs10012793	0.82[EUR][1000 genomes]
rs10021254	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10034669	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10155264	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10488840	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065745	1.00[ASN][1000 genomes]
rs16843803	1.00[ASN][1000 genomes]
rs16844026	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844028	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17780617	1.00[ASN][1000 genomes]
rs2003530	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2005787	0.96[EUR][1000 genomes]
rs28436280	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28507598	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025825	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34045730	1.00[ASN][1000 genomes]
rs34591077	1.00[ASN][1000 genomes]
rs362269	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362274	0.97[EUR][1000 genomes]
rs362276	0.90[EUR][1000 genomes]
rs362278	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362303	1.00[ASN][1000 genomes]
rs362304	1.00[ASN][1000 genomes]
rs362305	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362310	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362323	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362325	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs362338	0.99[EUR][1000 genomes]
rs363065	1.00[ASN][1000 genomes]
rs363069	1.00[ASN][1000 genomes]
rs363071	1.00[ASN][1000 genomes]
rs363078	1.00[ASN][1000 genomes]
rs363084	1.00[ASN][1000 genomes]
rs363087	1.00[ASN][1000 genomes]
rs363089	1.00[ASN][1000 genomes]
rs363090	0.92[EUR][1000 genomes]
rs363091	0.92[EUR][1000 genomes]
rs363093	0.92[EUR][1000 genomes]
rs363094	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363095	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363097	0.91[EUR][1000 genomes]
rs363098	0.99[EUR][1000 genomes]
rs363100	0.99[EUR][1000 genomes]
rs363101	0.96[EUR][1000 genomes]
rs363103	1.00[ASN][1000 genomes]
rs363105	1.00[ASN][1000 genomes]
rs363106	0.88[EUR][1000 genomes]
rs363124	0.92[EUR][1000 genomes]
rs363125	0.92[EUR][1000 genomes]
rs363128	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs363141	0.92[EUR][1000 genomes]
rs56794194	1.00[ASN][1000 genomes]
rs57196404	1.00[ASN][1000 genomes]
rs59588638	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61460614	1.00[ASN][1000 genomes]
rs61583241	1.00[ASN][1000 genomes]
rs61790489	1.00[ASN][1000 genomes]
rs61790490	1.00[ASN][1000 genomes]
rs61792472	1.00[ASN][1000 genomes]
rs61792477	1.00[ASN][1000 genomes]
rs61792500	1.00[ASN][1000 genomes]
rs61792501	1.00[ASN][1000 genomes]
rs61792502	1.00[ASN][1000 genomes]
rs61792503	1.00[ASN][1000 genomes]
rs61792505	1.00[ASN][1000 genomes]
rs61792507	1.00[ASN][1000 genomes]
rs61792508	1.00[ASN][1000 genomes]
rs61792509	1.00[ASN][1000 genomes]
rs61792510	1.00[ASN][1000 genomes]
rs61792512	1.00[ASN][1000 genomes]
rs61792515	1.00[ASN][1000 genomes]
rs61792531	1.00[ASN][1000 genomes]
rs61792532	1.00[ASN][1000 genomes]
rs61792533	1.00[ASN][1000 genomes]
rs61792535	0.86[EUR][1000 genomes]
rs6446724	0.99[EUR][1000 genomes]
rs6446725	0.99[EUR][1000 genomes]
rs6828615	0.90[EUR][1000 genomes]
rs6828882	0.97[EUR][1000 genomes]
rs6834455	0.90[EUR][1000 genomes]
rs6835567	0.91[EUR][1000 genomes]
rs6839081	0.92[EUR][1000 genomes]
rs6839274	0.99[EUR][1000 genomes]
rs6843895	0.90[EUR][1000 genomes]
rs73073018	1.00[ASN][1000 genomes]
rs7438553	0.95[EUR][1000 genomes]
rs7654034	0.92[EUR][1000 genomes]
rs7665816	0.90[EUR][1000 genomes]
rs7667354	0.99[EUR][1000 genomes]
rs7674122	1.00[ASN][1000 genomes]
rs7683309	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686771	1.00[ASN][1000 genomes]
rs7688390	0.86[EUR][1000 genomes]
rs7699037	1.00[ASN][1000 genomes]
rs9993781	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv461164	chr4:3149016-3215835	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv593439	chr4:3149016-3215835	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3114600-3292400	Weak transcription	Right Atrium	heart
2	chr4:3145800-3239200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr4:3167800-3203400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr4:3168000-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:3168000-3202800	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr4:3168000-3203000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr4:3170000-3208800	Weak transcription	Stomach Mucosa	stomach
8	chr4:3171200-3197600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:3171600-3193600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:3172000-3202800	Strong transcription	Duodenum Mucosa	Duodenum
11	chr4:3172200-3195400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr4:3172400-3199800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:3172400-3238800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:3172800-3202800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr4:3173600-3200000	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr4:3173800-3193400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:3174000-3204000	Strong transcription	Stomach Smooth Muscle	stomach
18	chr4:3176400-3199600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:3178400-3195200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr4:3178800-3200000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr4:3181000-3201400	Weak transcription	Hela-S3	cervix
22	chr4:3181200-3194000	Strong transcription	HSMM	muscle
23	chr4:3181200-3195200	Strong transcription	Fetal Stomach	stomach
24	chr4:3181600-3206600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:3182400-3203200	Strong transcription	Fetal Intestine Large	intestine
26	chr4:3183000-3197400	Strong transcription	Dnd41	blood
27	chr4:3183000-3202600	Strong transcription	Liver	Liver
28	chr4:3183400-3206800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:3185200-3208400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr4:3186000-3195600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:3188800-3193200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr4:3189000-3194400	Strong transcription	Fetal Muscle Leg	muscle
33	chr4:3189200-3199800	Strong transcription	Primary B cells from cord blood	blood
34	chr4:3189400-3193600	Strong transcription	Fetal Kidney	kidney
35	chr4:3189400-3194200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr4:3189600-3193400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:3189800-3194800	Strong transcription	Fetal Brain Female	brain
38	chr4:3190600-3203600	Weak transcription	Small Intestine	intestine
39	chr4:3191200-3196000	Weak transcription	Brain Substantia Nigra	brain
40	chr4:3191200-3201400	Weak transcription	Psoas Muscle	Psoas
41	chr4:3191200-3201400	Weak transcription	NHDF-Ad	bronchial
42	chr4:3191200-3203400	Weak transcription	Fetal Heart	heart
43	chr4:3191200-3208600	Weak transcription	A549	lung
44	chr4:3191400-3193200	Strong transcription	GM12878-XiMat	blood
45	chr4:3191400-3196600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr4:3191400-3197400	Weak transcription	Colonic Mucosa	Colon
47	chr4:3191600-3193400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr4:3191600-3193400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr4:3191600-3193400	Weak transcription	HMEC	breast
50	chr4:3191600-3193400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links