Variant report

Variant	rs2229773
Chromosome Location	chr17:38512480-38512481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:38512375-38512978	K562	blood:	n/a	n/a
2	POLR2A	chr17:38512390-38512578	HepG2	liver:	n/a	n/a
3	EGR1	chr17:38512311-38512591	K562	blood:	n/a	n/a
4	POLR2A	chr17:38509973-38514469	MCF-7	breast:	n/a	n/a
5	USF1	chr17:38512402-38512685	SK-N-SH_RA	brain:	n/a	n/a
6	POLR2A	chr17:38512376-38512995	HL-60	blood:	n/a	n/a
7	USF1	chr17:38512429-38512697	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr17:38512437-38512915	GM12878	blood:	n/a	n/a
9	USF1	chr17:38512421-38512730	H1-hESC	embryonic stem cell:	n/a	n/a
10	USF1	chr17:38512401-38512662	A549	lung:	n/a	n/a
11	USF1	chr17:38512365-38512690	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38461366..38465134-chr17:38511894..38515079,3	K562	blood:
2	chr17:38511730..38513729-chr17:38571391..38573347,2	MCF-7	breast:
3	chr17:38510766..38512745-chr17:38518464..38520591,2	MCF-7	breast:
4	chr17:38511733..38514240-chr17:38577131..38579483,2	K562	blood:
5	chr17:38511765..38516691-chr17:38517275..38519964,6	K562	blood:
6	chr17:38508440..38510370-chr17:38512400..38513964,2	MCF-7	breast:
7	chr17:38512119..38512637-chr17:38606414..38607097,2	K562	blood:
8	chr17:38498880..38501087-chr17:38510069..38512675,2	MCF-7	breast:
9	chr17:38457066..38460899-chr17:38504442..38513119,13	K562	blood:
10	chr17:38512328..38514816-chr17:38599372..38601373,2	K562	blood:
11	chr17:38512350..38514701-chr17:38725201..38727285,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000266208	TF binding region
ENSG00000183153	Chromatin interaction
ENSG00000270145	Chromatin interaction
ENSG00000265666	Chromatin interaction
ENSG00000141753	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10305288	1.00[AFR][1000 genomes]
rs10305296	1.00[AFR][1000 genomes]
rs10305303	1.00[AFR][1000 genomes]
rs10512482	0.92[EUR][1000 genomes]
rs1104761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11540720	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11867902	1.00[CEU][hapmap]
rs12103533	0.92[EUR][1000 genomes]
rs15685	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16965660	0.92[EUR][1000 genomes]
rs16965669	0.92[EUR][1000 genomes]
rs16965734	0.92[EUR][1000 genomes]
rs16965736	0.92[EUR][1000 genomes]
rs16965748	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965774	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs16965778	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17557495	1.00[AFR][1000 genomes]
rs17616365	1.00[AMR][1000 genomes]
rs17616543	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17616879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17617263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17618397	1.00[AFR][1000 genomes]
rs17678817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678959	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17678990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679038	1.00[AFR][1000 genomes]
rs17679086	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17679361	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680410	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17680685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17680704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2012667	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28362320	0.92[EUR][1000 genomes]
rs28362321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28526298	0.92[EUR][1000 genomes]
rs33998939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34270904	0.92[EUR][1000 genomes]
rs34300454	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs35783632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35898909	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41283417	0.92[EUR][1000 genomes]
rs41283423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4134998	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135019	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135021	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135027	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4135030	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45612441	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7214783	0.85[EUR][1000 genomes]
rs72819623	1.00[AFR][1000 genomes]
rs72819624	1.00[AFR][1000 genomes]
rs72819628	1.00[AFR][1000 genomes]
rs72819630	1.00[AFR][1000 genomes]
rs72819632	1.00[AFR][1000 genomes]
rs72819633	1.00[AFR][1000 genomes]
rs72819651	1.00[AFR][1000 genomes]
rs8067519	0.92[EUR][1000 genomes]
rs8071687	0.92[EUR][1000 genomes]
rs8077482	0.92[EUR][1000 genomes]
rs9889905	0.92[EUR][1000 genomes]
rs9891944	1.00[EUR][1000 genomes]
rs9894364	0.92[EUR][1000 genomes]
rs9894807	0.92[EUR][1000 genomes]
rs9898500	0.92[EUR][1000 genomes]
rs9899425	0.92[EUR][1000 genomes]
rs9900154	0.92[EUR][1000 genomes]
rs9903293	0.92[EUR][1000 genomes]
rs9906274	1.00[EUR][1000 genomes]
rs9909777	0.92[EUR][1000 genomes]
rs9909811	0.92[EUR][1000 genomes]
rs9910373	0.92[EUR][1000 genomes]
rs9915775	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv908222	chr17:38504241-38526973	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38503200-38512600	Genic enhancers	Spleen	Spleen
2	chr17:38503600-38513000	Genic enhancers	A549	lung
3	chr17:38503800-38513600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr17:38504400-38514000	Genic enhancers	Fetal Muscle Trunk	muscle
5	chr17:38504400-38514200	Genic enhancers	Fetal Muscle Leg	muscle
6	chr17:38504800-38513000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr17:38505000-38513600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr17:38505200-38518600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:38505400-38513000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr17:38505400-38514200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr17:38505600-38512800	Strong transcription	Primary T cells from cord blood	blood
12	chr17:38506200-38515000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr17:38506400-38513000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:38506800-38512800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:38506800-38512800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
16	chr17:38506800-38513400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr17:38507000-38513400	Strong transcription	Gastric	stomach
18	chr17:38507000-38514600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr17:38507200-38512600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:38507200-38513000	Strong transcription	NHEK	skin
21	chr17:38507200-38513600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:38507400-38514000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr17:38508000-38512600	Strong transcription	Esophagus	oesophagus
24	chr17:38508200-38514200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:38508200-38515000	Weak transcription	Brain Substantia Nigra	brain
26	chr17:38508600-38513000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr17:38508800-38512800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:38508800-38519000	Weak transcription	Psoas Muscle	Psoas
29	chr17:38509000-38512600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr17:38509000-38513000	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr17:38509000-38514600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:38509200-38513600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:38509200-38514600	Weak transcription	Brain Anterior Caudate	brain
34	chr17:38509200-38518400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:38509200-38518400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr17:38509400-38512600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr17:38509400-38515000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr17:38509600-38513400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr17:38509600-38514800	Weak transcription	Dnd41	blood
40	chr17:38509600-38515000	Weak transcription	Brain Angular Gyrus	brain
41	chr17:38509800-38515000	Weak transcription	NHDF-Ad	bronchial
42	chr17:38510400-38512800	Enhancers	Fetal Heart	heart
43	chr17:38510400-38513000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:38510400-38513000	Enhancers	Fetal Brain Male	brain
45	chr17:38510400-38514000	Genic enhancers	Fetal Stomach	stomach
46	chr17:38510600-38512600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr17:38510600-38513000	Genic enhancers	Ovary	ovary
48	chr17:38510600-38514800	Weak transcription	NH-A	brain
49	chr17:38510800-38512800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:38510800-38512800	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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