Variant report

Variant	rs11904619
Chromosome Location	chr2:233720166-233720167
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	chr2:233718747..233721195-chr2:233739354..233741020,2	MCF-7	breast:
2	chr2:233719856..233720631-chr4:71847376..71848070,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182600	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10178713	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207739	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11679581	0.80[AMR][1000 genomes]
rs11684636	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11689661	1.00[JPT][hapmap]
rs12052869	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12328140	0.95[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328151	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12694915	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12992588	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13012585	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035517	0.91[CEU][hapmap];0.86[CHB][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13383733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13387762	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13401578	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13408229	1.00[JPT][hapmap]
rs13424896	0.90[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13425918	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446307	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2044450	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2048866	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2289914	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs2289915	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs2292724	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292725	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2293782	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs28491817	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34063802	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs34652626	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35141217	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62193305	0.80[AMR][1000 genomes]
rs6747479	0.95[CEU][hapmap]
rs73005582	0.80[AMR][1000 genomes]
rs9288675	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9288676	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948470	chr2:233166262-233886732	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1005123	chr2:233227729-233920152	Enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv536173	chr2:233227729-233920152	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv834570	chr2:233639160-233805067	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv584697	chr2:233684097-233733352	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1009825	chr2:233709566-233763470	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233665800-233734200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:233667600-233726400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233689200-233726400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:233698400-233723600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:233701000-233729200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr2:233703400-233726400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:233703400-233726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:233703600-233725200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:233703800-233724800	Strong transcription	Dnd41	blood
10	chr2:233704000-233721400	Strong transcription	Fetal Intestine Large	intestine
11	chr2:233704200-233725000	Strong transcription	Fetal Thymus	thymus
12	chr2:233704400-233726200	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr2:233704400-233726600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:233704600-233726000	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:233704600-233728000	Strong transcription	Primary T cells from cord blood	blood
16	chr2:233704800-233726600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:233705000-233726600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr2:233705600-233726600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:233705600-233727800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr2:233712000-233721400	Strong transcription	Fetal Intestine Small	intestine
21	chr2:233712000-233728200	Strong transcription	Fetal Stomach	stomach
22	chr2:233713400-233721400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:233713600-233721600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:233714000-233726400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:233714800-233721400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:233714800-233721400	Weak transcription	Fetal Brain Male	brain
27	chr2:233715200-233721200	Weak transcription	Right Ventricle	heart
28	chr2:233715200-233721400	Weak transcription	Stomach Mucosa	stomach
29	chr2:233715800-233721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr2:233715800-233725400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:233716000-233720200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:233716000-233721200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:233716200-233720200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:233716800-233720200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:233716800-233720800	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:233716800-233721000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:233717000-233720200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:233717000-233720800	Weak transcription	Spleen	Spleen
39	chr2:233717000-233721000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:233717000-233721000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:233717000-233721200	Weak transcription	Brain Angular Gyrus	brain
42	chr2:233717000-233721200	Weak transcription	Left Ventricle	heart
43	chr2:233717000-233721200	Weak transcription	Pancreas	Pancrea
44	chr2:233717000-233721200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:233717000-233721400	Weak transcription	Aorta	Aorta
46	chr2:233717000-233721400	Weak transcription	Gastric	stomach
47	chr2:233717000-233721600	Weak transcription	Esophagus	oesophagus
48	chr2:233717000-233721600	Enhancers	HSMMtube	muscle
49	chr2:233717400-233721400	Enhancers	Liver	Liver
50	chr2:233717600-233721000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links