Variant report

Variant	rs3008643
Chromosome Location	chr1:222749171-222749172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:222748508..222750746-chr1:222752040..222754517,3	K562	blood:
2	chr1:222747881..222749778-chr1:222751683..222754115,2	MCF-7	breast:
3	chr1:222748011..222750721-chr1:222758316..222760837,2	MCF-7	breast:
4	chr1:222746416..222749268-chr1:222884399..222887306,2	K562	blood:

Variant related genes	Relation type
ENSG00000162819	Chromatin interaction
ENSG00000186063	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2936028	1.00[AFR][1000 genomes]
rs2936029	1.00[AFR][1000 genomes]
rs2936042	1.00[AFR][1000 genomes]
rs2936043	1.00[AFR][1000 genomes]
rs2936053	1.00[AFR][1000 genomes]
rs3002127	1.00[AFR][1000 genomes]
rs3002135	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3002153	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3008619	1.00[AFR][1000 genomes]
rs3008636	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs3008646	1.00[AFR][1000 genomes]
rs3008648	0.87[AFR][1000 genomes]
rs3008649	1.00[AFR][1000 genomes]
rs3008652	1.00[AFR][1000 genomes]
rs35877231	1.00[AFR][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	nsv873203	chr1:222332906-222775000	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv873205	chr1:222718718-222923351	Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1842070	chr1:222732027-222763235	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222720800-222757400	Weak transcription	HSMMtube	muscle
2	chr1:222721200-222762200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:222721800-222762400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:222722000-222755600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:222722000-222755800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:222724800-222750800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:222725600-222762200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:222727600-222762600	Weak transcription	Aorta	Aorta
9	chr1:222727800-222762400	Weak transcription	Thymus	Thymus
10	chr1:222728200-222762200	Weak transcription	Small Intestine	intestine
11	chr1:222729600-222762400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:222729800-222758800	Weak transcription	Pancreas	Pancrea
13	chr1:222730800-222760200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:222730800-222761200	Weak transcription	Fetal Brain Male	brain
15	chr1:222731200-222762400	Weak transcription	Spleen	Spleen
16	chr1:222731600-222756200	Weak transcription	Esophagus	oesophagus
17	chr1:222731600-222758800	Weak transcription	Gastric	stomach
18	chr1:222731600-222762200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:222733600-222762400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:222733800-222761800	Weak transcription	Brain Angular Gyrus	brain
21	chr1:222733800-222762200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:222734000-222762400	Weak transcription	Right Ventricle	heart
23	chr1:222734200-222762400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr1:222734800-222750200	Weak transcription	HUVEC	blood vessel
25	chr1:222734800-222762200	Weak transcription	Colonic Mucosa	Colon
26	chr1:222738200-222753400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:222739000-222761600	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:222739200-222753200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:222739600-222751000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:222740000-222752600	Strong transcription	Dnd41	blood
31	chr1:222741200-222753200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:222742200-222755000	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:222742200-222762400	Weak transcription	Fetal Kidney	kidney
34	chr1:222742600-222755000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr1:222742600-222755800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:222742800-222749800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:222742800-222749800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:222742800-222755600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:222742800-222755600	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:222742800-222759600	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:222742800-222760200	Weak transcription	Psoas Muscle	Psoas
42	chr1:222742800-222762200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:222743000-222762400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:222743200-222755600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:222743200-222755800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:222743400-222750200	Weak transcription	NHDF-Ad	bronchial
47	chr1:222743400-222755000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:222743400-222759400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:222743400-222761600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr1:222743600-222755600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links