Variant report

Variant	rs6447660
Chromosome Location	chr4:48772680-48772681
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48772120..48774246-chr4:48777185..48779870,3	MCF-7	breast:
2	chr4:48772504..48776956-chr4:48777763..48782974,9	K562	blood:
3	chr4:48772195..48774601-chr4:48832586..48834543,2	K562	blood:

Variant related genes	Relation type
ENSG00000109180	Chromatin interaction
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11939889	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11943219	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13119414	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1517674	0.80[ASN][1000 genomes]
rs1980193	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2056201	0.81[ASN][1000 genomes]
rs2176460	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2354314	0.81[EUR][1000 genomes]
rs4695397	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4695400	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695401	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57797824	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62309747	0.83[AMR][1000 genomes]
rs6447655	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6830078	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6853588	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7657332	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657698	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7680280	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7681070	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7697522	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs955683	0.81[EUR][1000 genomes]
rs9790336	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised 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	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6447660	SLC10A4	cis	lung	GTEx
rs6447660	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48731600-48779800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:48747200-48777200	Weak transcription	Fetal Intestine Small	intestine
3	chr4:48751600-48777200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr4:48754800-48774200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:48755000-48773600	Weak transcription	Aorta	Aorta
6	chr4:48755200-48774200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr4:48755400-48775600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:48755600-48774800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr4:48756000-48773000	Weak transcription	HUVEC	blood vessel
10	chr4:48756000-48774800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:48756200-48774200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:48759000-48775600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:48759000-48778600	Weak transcription	Fetal Stomach	stomach
14	chr4:48759200-48775400	Weak transcription	NHEK	skin
15	chr4:48759200-48775600	Weak transcription	HMEC	breast
16	chr4:48761000-48779800	Weak transcription	Placenta	Placenta
17	chr4:48762000-48775200	Weak transcription	Fetal Lung	lung
18	chr4:48762000-48777200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:48763000-48779800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr4:48764000-48775000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr4:48764200-48773600	Weak transcription	Right Ventricle	heart
22	chr4:48764400-48773000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr4:48764600-48774400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr4:48764600-48779800	Weak transcription	HSMM	muscle
25	chr4:48764800-48773600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:48766000-48774800	Weak transcription	Dnd41	blood
27	chr4:48766600-48779800	Weak transcription	Ovary	ovary
28	chr4:48767000-48779800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr4:48767400-48775600	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:48768000-48780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:48768600-48772800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:48768600-48773200	Weak transcription	Colon Smooth Muscle	Colon
33	chr4:48768600-48773600	Weak transcription	Psoas Muscle	Psoas
34	chr4:48768600-48774800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr4:48768600-48774800	Weak transcription	Small Intestine	intestine
36	chr4:48768600-48775600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:48768600-48775600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr4:48768600-48775600	Weak transcription	Right Atrium	heart
39	chr4:48768600-48775600	Weak transcription	Spleen	Spleen
40	chr4:48768600-48777200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:48768600-48777200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:48768600-48780000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr4:48768600-48780800	Weak transcription	Gastric	stomach
44	chr4:48768800-48773000	Weak transcription	Adipose Nuclei	Adipose
45	chr4:48768800-48773000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr4:48768800-48774200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr4:48768800-48775200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:48768800-48775600	Weak transcription	Thymus	Thymus
49	chr4:48768800-48777200	Weak transcription	Fetal Intestine Large	intestine
50	chr4:48768800-48780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links