Variant report

Variant	rs1228039
Chromosome Location	chr11:48024976-48024977
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:48023010..48025902-chr11:48026149..48029415,3	K562	blood:
2	chr11:48017179..48020205-chr11:48021877..48026415,4	K562	blood:
3	chr11:48018299..48021070-chr11:48022717..48025055,2	MCF-7	breast:
4	chr11:48002272..48005145-chr11:48021590..48026495,6	K562	blood:
5	chr11:48024330..48026388-chr11:48082917..48084428,2	K562	blood:
6	chr11:48002272..48005395-chr11:48022576..48027269,4	K562	blood:
7	chr11:48023169..48025909-chr11:48028991..48031119,2	K562	blood:

Variant related genes	Relation type
ENSG00000149177	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1228026	1.00[EUR][1000 genomes]
rs1228028	0.90[YRI][hapmap];1.00[EUR][1000 genomes]
rs1228031	0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228032	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228036	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1228038	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228040	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs1228042	1.00[EUR][1000 genomes]
rs1234904	0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1237924	1.00[EUR][1000 genomes]
rs1238706	0.90[YRI][hapmap]
rs1630025	1.00[EUR][1000 genomes]
rs1681623	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1681624	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1681625	1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1729286	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1729287	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1729288	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1729291	0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2626565	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2930193	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs2930194	1.00[EUR][1000 genomes]
rs2930197	1.00[EUR][1000 genomes]
rs2950891	1.00[EUR][1000 genomes]
rs73462886	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
12	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv528641	chr11:48004369-48043053	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
15	nsv869124	chr11:48014539-48783113	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
16	nsv1051805	chr11:48016488-48378048	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48013200-48025600	Weak transcription	HSMMtube	muscle
2	chr11:48013400-48025200	Weak transcription	Left Ventricle	heart
3	chr11:48013400-48025800	Weak transcription	Fetal Stomach	stomach
4	chr11:48013400-48027200	Weak transcription	Aorta	Aorta
5	chr11:48018000-48025800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:48018200-48025800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:48018400-48026200	Weak transcription	Adipose Nuclei	Adipose
8	chr11:48018400-48026800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr11:48018800-48042000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr11:48019000-48025400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr11:48019000-48025600	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr11:48019000-48027200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:48019200-48025200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr11:48019200-48026000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:48019400-48025600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:48019400-48027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr11:48019600-48025600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:48019600-48025800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:48019600-48025800	Weak transcription	Placenta	Placenta
20	chr11:48020000-48027000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr11:48020400-48027000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:48020400-48027400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:48020600-48029800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr11:48020800-48025600	Enhancers	Primary B cells from cord blood	blood
25	chr11:48020800-48025600	Weak transcription	Fetal Kidney	kidney
26	chr11:48020800-48025600	Weak transcription	HSMM	muscle
27	chr11:48020800-48027400	Weak transcription	Pancreas	Pancrea
28	chr11:48021000-48027400	Weak transcription	Colonic Mucosa	Colon
29	chr11:48021000-48029800	Enhancers	Liver	Liver
30	chr11:48022000-48027400	Weak transcription	Fetal Muscle Leg	muscle
31	chr11:48022800-48025000	Enhancers	Brain Angular Gyrus	brain
32	chr11:48022800-48026000	Weak transcription	Lung	lung
33	chr11:48022800-48027200	Weak transcription	Thymus	Thymus
34	chr11:48023000-48025000	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr11:48023000-48025200	Weak transcription	Fetal Heart	heart
36	chr11:48023000-48025600	Weak transcription	Small Intestine	intestine
37	chr11:48023000-48027400	Weak transcription	Fetal Intestine Large	intestine
38	chr11:48023200-48026000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr11:48023200-48028400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:48023200-48028400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:48023400-48025200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:48023400-48025200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:48023400-48025800	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr11:48023400-48026000	Weak transcription	Stomach Mucosa	stomach
45	chr11:48023400-48026800	Weak transcription	Fetal Intestine Small	intestine
46	chr11:48023400-48026800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:48023400-48027200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:48023400-48027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:48023400-48027400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:48023600-48025400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links