Variant report

Variant	rs12004561
Chromosome Location	chr9:103075010-103075011
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:103074390-103075485	K562	blood:	n/a	n/a
2	POLR2A	chr9:103074733-103075364	GM12878	blood:	n/a	n/a
3	SETDB1	chr9:103074566-103075060	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:103069740..103072303-chr9:103072718..103076064,3	K562	blood:

Variant related genes	Relation type
TEX10	TF binding region
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11998846	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs11999065	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11999333	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11999405	1.00[AMR][1000 genomes]
rs11999630	1.00[YRI][hapmap]
rs11999759	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11999920	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12000423	1.00[AMR][1000 genomes]
rs12000833	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12001165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12001197	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12001218	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12001575	1.00[AMR][1000 genomes]
rs12003270	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12003337	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12003593	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs12005084	1.00[AMR][1000 genomes]
rs12005328	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12005758	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28704948	1.00[AMR][1000 genomes]
rs58290582	1.00[AMR][1000 genomes]
rs58604350	1.00[AMR][1000 genomes]
rs59127855	1.00[AMR][1000 genomes]
rs61163672	1.00[AMR][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	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103044600-103102400	Weak transcription	Stomach Mucosa	stomach
2	chr9:103046000-103075400	Strong transcription	Primary T cells fromperipheralblood	blood
3	chr9:103046400-103104000	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:103046600-103092400	Strong transcription	Fetal Thymus	thymus
5	chr9:103048000-103078000	Strong transcription	Primary T cells from cord blood	blood
6	chr9:103048400-103083000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:103050600-103086400	Strong transcription	Dnd41	blood
8	chr9:103050800-103080400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr9:103051000-103088800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:103051200-103078000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:103055800-103077600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr9:103057600-103112600	Weak transcription	Fetal Brain Male	brain
13	chr9:103058400-103092200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:103058800-103084800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:103063800-103093400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:103063800-103106000	Weak transcription	Esophagus	oesophagus
17	chr9:103064000-103100000	Weak transcription	Colonic Mucosa	Colon
18	chr9:103064200-103093200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr9:103064600-103079400	Weak transcription	HSMMtube	muscle
20	chr9:103064800-103104200	Weak transcription	Right Ventricle	heart
21	chr9:103065000-103080600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr9:103065000-103114200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:103065200-103087600	Weak transcription	Brain Anterior Caudate	brain
24	chr9:103065400-103080200	Weak transcription	Brain Substantia Nigra	brain
25	chr9:103065400-103087400	Weak transcription	Psoas Muscle	Psoas
26	chr9:103066200-103080200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:103066200-103087800	Weak transcription	Gastric	stomach
28	chr9:103066200-103088400	Weak transcription	Lung	lung
29	chr9:103066200-103100400	Weak transcription	Aorta	Aorta
30	chr9:103066200-103112600	Weak transcription	Pancreas	Pancrea
31	chr9:103066200-103113200	Weak transcription	Spleen	Spleen
32	chr9:103066200-103113800	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr9:103066400-103079400	Weak transcription	HUVEC	blood vessel
34	chr9:103066600-103080400	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:103066800-103091600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr9:103067000-103086600	Strong transcription	Primary B cells from cord blood	blood
37	chr9:103067600-103112400	Weak transcription	Small Intestine	intestine
38	chr9:103067800-103080800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr9:103068000-103077400	Weak transcription	Liver	Liver
40	chr9:103068200-103080400	Weak transcription	Brain Angular Gyrus	brain
41	chr9:103068200-103085200	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:103068200-103094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:103068600-103077400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:103069000-103075200	Strong transcription	Placenta	Placenta
45	chr9:103069200-103095400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
46	chr9:103069400-103075400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr9:103069400-103094800	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr9:103069800-103078400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:103069800-103078800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr9:103069800-103092000	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links