Variant report

Variant	rs6789862
Chromosome Location	chr3:137911687-137911688
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:137893115..137894749-chr3:137909157..137912664,3	K562	blood:
2	chr3:137892199..137894619-chr3:137909781..137912615,2	K562	blood:
3	chr3:137905805..137908807-chr3:137910538..137912861,3	MCF-7	breast:
4	chr3:137904054..137908081-chr3:137908152..137912895,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction
ENSG00000114098	Chromatin interaction

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

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

rs_ID	r²[population]
rs11917468	1.00[MEX][hapmap]
rs11921619	1.00[MEX][hapmap]
rs16847931	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3886726	1.00[MEX][hapmap];0.91[YRI][hapmap]
rs3963416	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6439801	1.00[MEX][hapmap]
rs6439802	1.00[MEX][hapmap]
rs6783016	0.95[YRI][hapmap]
rs6790420	1.00[MEX][hapmap]
rs6790428	1.00[MEX][hapmap]
rs6796118	1.00[MEX][hapmap]
rs6796663	0.86[YRI][hapmap]
rs6797207	0.86[YRI][hapmap]
rs7631817	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7637825	0.81[AMR][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137907200-137916000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:137907200-137919800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:137907600-137913400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:137907600-137915400	Weak transcription	Left Ventricle	heart
5	chr3:137907600-137915800	Weak transcription	Gastric	stomach
6	chr3:137907600-137921800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:137907600-137922200	Weak transcription	Esophagus	oesophagus
8	chr3:137907600-137929400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:137907600-137941600	Weak transcription	Lung	lung
10	chr3:137907600-137942200	Weak transcription	Pancreas	Pancrea
11	chr3:137907600-137942400	Weak transcription	Spleen	Spleen
12	chr3:137907800-137913400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:137907800-137913600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:137907800-137915000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:137907800-137915200	Weak transcription	NH-A	brain
16	chr3:137907800-137915400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:137907800-137916000	Weak transcription	Ovary	ovary
18	chr3:137907800-137922200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:137907800-137922400	Weak transcription	Thymus	Thymus
20	chr3:137907800-137925400	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:137907800-137941000	Weak transcription	Fetal Kidney	kidney
22	chr3:137908000-137913600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:137908000-137922200	Weak transcription	Adipose Nuclei	Adipose
24	chr3:137908000-137922200	Weak transcription	Aorta	Aorta
25	chr3:137908000-137922200	Weak transcription	HSMMtube	muscle
26	chr3:137908000-137929200	Weak transcription	NHLF	lung
27	chr3:137908000-137940400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:137908200-137940600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:137908400-137913600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr3:137908400-137929200	Weak transcription	Osteobl	bone
31	chr3:137908400-137941600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:137908400-137942200	Weak transcription	NHDF-Ad	bronchial
33	chr3:137908400-137942400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:137908400-137956200	Weak transcription	A549	lung
35	chr3:137908600-137911800	Strong transcription	Primary hematopoietic stem cells	blood
36	chr3:137908600-137913600	Weak transcription	Brain Substantia Nigra	brain
37	chr3:137908600-137914200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:137908600-137914800	Weak transcription	Brain Anterior Caudate	brain
39	chr3:137908600-137915000	Weak transcription	Primary B cells from cord blood	blood
40	chr3:137908600-137916000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:137908600-137918800	Weak transcription	Right Ventricle	heart
42	chr3:137908600-137924000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:137908800-137911800	Strong transcription	HSMM	muscle
44	chr3:137908800-137914200	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:137908800-137914400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr3:137908800-137931000	Weak transcription	HUVEC	blood vessel
47	chr3:137908800-137941800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr3:137908800-137942200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:137909000-137911800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr3:137909000-137912200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links