Variant report

Variant	rs28730892
Chromosome Location	chr22:30196264-30196265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30191545..30194644-chr22:30195667..30197802,3	K562	blood:
2	chr22:30161539..30163655-chr22:30194119..30196895,2	K562	blood:
3	chr22:30192738..30197507-chr22:30207918..30212414,7	MCF-7	breast:
4	chr22:30160556..30163537-chr22:30195523..30197184,3	MCF-7	breast:
5	chr22:30193309..30197041-chr22:30202385..30207780,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100319	Chromatin interaction
ENSG00000184076	Chromatin interaction
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1071962	0.88[ASN][1000 genomes]
rs12158466	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12159277	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12159536	0.82[EUR][1000 genomes]
rs12163073	0.82[EUR][1000 genomes]
rs12627866	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12628028	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12628234	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12628294	0.84[ASN][1000 genomes]
rs12628545	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs14115	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16987142	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16988049	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17711461	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17711508	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2018808	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240364	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240365	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2240366	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs249399	0.96[ASN][1000 genomes]
rs249402	0.82[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs57122143	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58015017	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59394320	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997515	0.82[EUR][1000 genomes]
rs5997518	0.90[EUR][1000 genomes]
rs5997519	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5997520	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5997524	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6006234	0.82[EUR][1000 genomes]
rs6006235	0.82[EUR][1000 genomes]
rs6006238	0.82[EUR][1000 genomes]
rs6006239	0.82[EUR][1000 genomes]
rs6006241	0.90[EUR][1000 genomes]
rs6006242	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6006247	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006249	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006250	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6006262	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805530	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61616383	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61736786	0.84[ASN][1000 genomes]
rs7285660	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7285800	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7287777	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7289250	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7290420	0.82[EUR][1000 genomes]
rs73392899	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73394814	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394831	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73394838	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs737721	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs737728	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs740116	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138165	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv1829662	chr22:30171725-30304390	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	esv1829425	chr22:30184378-30297376	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 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	chr22:30177600-30233000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:30182200-30217000	Strong transcription	Fetal Intestine Small	intestine
3	chr22:30182200-30222200	Strong transcription	Thymus	Thymus
4	chr22:30182800-30204600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr22:30182800-30204800	Strong transcription	Fetal Brain Female	brain
6	chr22:30182800-30232200	Strong transcription	Primary T cells from cord blood	blood
7	chr22:30182800-30232200	Strong transcription	Fetal Stomach	stomach
8	chr22:30183000-30221400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr22:30183200-30197000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr22:30183200-30230800	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr22:30183400-30204800	Strong transcription	Brain Germinal Matrix	brain
12	chr22:30183400-30224000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr22:30183400-30230800	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr22:30183800-30204800	Strong transcription	Ovary	ovary
15	chr22:30183800-30205000	Strong transcription	Fetal Intestine Large	intestine
16	chr22:30183800-30205200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:30183800-30224000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr22:30183800-30232200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr22:30184000-30198400	Strong transcription	Primary T helper cells PMA-I stimulated	--
20	chr22:30184000-30204800	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr22:30184000-30222200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr22:30186600-30199800	Weak transcription	Fetal Kidney	kidney
23	chr22:30189400-30197200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:30189600-30201000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr22:30189600-30201800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:30189800-30197600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr22:30189800-30201800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr22:30191000-30222200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr22:30191600-30196400	Genic enhancers	Placenta	Placenta
30	chr22:30191600-30198400	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr22:30192000-30196800	Weak transcription	Small Intestine	intestine
32	chr22:30192200-30197000	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr22:30192400-30198200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr22:30192600-30198400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr22:30192800-30196400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr22:30192800-30196600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr22:30193400-30217200	Strong transcription	Fetal Thymus	thymus
38	chr22:30194000-30197800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr22:30194000-30198000	Genic enhancers	Left Ventricle	heart
40	chr22:30194000-30198200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr22:30194000-30198400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
42	chr22:30194000-30198400	Genic enhancers	Gastric	stomach
43	chr22:30194000-30198600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr22:30194200-30197000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr22:30194200-30197600	Enhancers	Right Atrium	heart
46	chr22:30194200-30198200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr22:30194200-30212200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr22:30194400-30197000	Genic enhancers	Dnd41	blood
49	chr22:30194400-30197800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr22:30194400-30198400	Genic enhancers	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links