Variant report

Variant	rs6897978
Chromosome Location	chr5:118789338-118789339
allele	A/G
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	GATA1	chr5:118788092-118789851	PBDE	blood:	n/a	chr5:118788628-118788637 chr5:118788628-118788635 chr5:118788847-118788859 chr5:118788627-118788637
2	POLR2A	chr5:118788062-118790211	HepG2	liver:	n/a	n/a
3	NR2F2	chr5:118788780-118789424	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:118787604-118790194	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:118323861..118326778-chr5:118787539..118789741,2	MCF-7	breast:
2	chr5:118788483..118791355-chr5:118802793..118805177,3	K562	blood:
3	chr5:118787302..118789344-chr5:118814419..118817189,2	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000239084	Chromatin interaction
ENSG00000133835	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10059654	0.88[ASN][1000 genomes]
rs10478424	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.83[YRI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11205	0.82[CHB][hapmap]
rs11241507	0.82[CHB][hapmap]
rs1155777	0.82[CHB][hapmap]
rs150938	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs257969	0.82[JPT][hapmap]
rs257985	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2914210	0.82[CHB][hapmap]
rs3797368	0.85[CHB][hapmap]
rs3797372	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv4974	chr5:118750259-118795376	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr5:118787400-118789400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr5:118787800-118789400	Active TSS	H1 Cell Line	embryonic stem cell
3	chr5:118787800-118789400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr5:118787800-118789400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:118787800-118789400	Active TSS	HSMMtube	muscle
6	chr5:118787800-118789400	Active TSS	NH-A	brain
7	chr5:118787800-118790000	Active TSS	Fetal Brain Male	brain
8	chr5:118787800-118790200	Active TSS	Aorta	Aorta
9	chr5:118788000-118789400	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr5:118788000-118789400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:118788000-118789400	Active TSS	Psoas Muscle	Psoas
12	chr5:118788000-118789600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr5:118788000-118789600	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr5:118788000-118789800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:118788000-118790000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:118788000-118790000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:118788400-118789600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:118788600-118789400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr5:118788600-118789400	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr5:118788600-118789400	Flanking Active TSS	Dnd41	blood
21	chr5:118788600-118789400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr5:118788800-118789400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr5:118788800-118789400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr5:118788800-118789400	Flanking Active TSS	Fetal Brain Female	brain
25	chr5:118788800-118789400	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr5:118788800-118789400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
27	chr5:118788800-118789400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:118788800-118789400	Flanking Active TSS	Hela-S3	cervix
29	chr5:118788800-118789400	Flanking Active TSS	Osteobl	bone
30	chr5:118788800-118789600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:118788800-118789600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:118788800-118789600	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr5:118788800-118789600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
34	chr5:118788800-118789800	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr5:118788800-118791000	Flanking Active TSS	Liver	Liver
36	chr5:118789000-118789400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:118789000-118789400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr5:118789000-118789400	Enhancers	Primary B cells from peripheral blood	blood
39	chr5:118789000-118789400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:118789000-118789400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr5:118789000-118789400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:118789000-118789400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr5:118789000-118789400	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr5:118789000-118789400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr5:118789000-118789400	Flanking Active TSS	Fetal Heart	heart
46	chr5:118789000-118789400	Flanking Active TSS	Fetal Intestine Small	intestine
47	chr5:118789000-118789400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr5:118789000-118789400	Flanking Active TSS	Fetal Lung	lung
49	chr5:118789000-118789400	Flanking Active TSS	Rectal Smooth Muscle	rectum
50	chr5:118789000-118789400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links