Variant report

Variant	rs9348119
Chromosome Location	chr6:166743760-166743761
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a
2	IRF1	chr6:166743274-166743823	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:166742537..166744079-chr6:166803763..166806576,2	K562	blood:
2	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
3	chr6:166689019..166690684-chr6:166742246..166744543,2	K562	blood:
4	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:

No data

Variant related genes	Relation type
HNRNPA1P49	TF binding region
SFT2D1	TF binding region
ENSG00000198818	Chromatin interaction
ENSG00000060762	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10455809	0.83[CHB][hapmap]
rs10455977	0.81[CHB][hapmap]
rs10946158	0.87[CHB][hapmap]
rs11752886	0.87[CHB][hapmap]
rs11755305	0.83[CHB][hapmap]
rs12198613	0.87[CHB][hapmap]
rs12209616	0.87[ASN][1000 genomes]
rs12214812	0.87[CHB][hapmap]
rs1830558	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4144886	0.87[CHB][hapmap]
rs4144887	0.87[CHB][hapmap]
rs4144888	0.87[CHB][hapmap]
rs4709111	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4710042	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68016351	0.87[ASN][1000 genomes]
rs6916128	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7088	1.00[ASN][1000 genomes]
rs73263155	0.87[ASN][1000 genomes]
rs73788236	0.87[ASN][1000 genomes]
rs7767887	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs927190	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9347123	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348121	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9355571	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366004	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941683	0.87[CHB][hapmap]
rs9459653	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9348119	LOC135043	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166723200-166744200	Weak transcription	Right Atrium	heart
2	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:166729200-166744200	Weak transcription	Stomach Mucosa	stomach
4	chr6:166729600-166744000	Weak transcription	Small Intestine	intestine
5	chr6:166730400-166744200	Weak transcription	Fetal Brain Male	brain
6	chr6:166732400-166744000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:166733200-166744400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
11	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
12	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
13	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
14	chr6:166737000-166745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr6:166738200-166754200	Weak transcription	NH-A	brain
16	chr6:166739400-166744400	Weak transcription	Brain Angular Gyrus	brain
17	chr6:166739400-166745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:166739400-166748000	Weak transcription	Gastric	stomach
20	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:166739800-166743800	Weak transcription	NHLF	lung
22	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
23	chr6:166740200-166743800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr6:166740200-166744000	Weak transcription	Right Ventricle	heart
25	chr6:166740200-166744200	Weak transcription	A549	lung
26	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
27	chr6:166740800-166744000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:166741000-166744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr6:166741400-166743800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:166741400-166744200	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:166741400-166744200	Weak transcription	Esophagus	oesophagus
32	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:166741400-166750000	Weak transcription	HMEC	breast
34	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:166741600-166744200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:166742200-166744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr6:166742400-166744000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr6:166742400-166744000	Weak transcription	Pancreas	Pancrea
42	chr6:166742400-166744400	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:166742400-166744800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:166742600-166743800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:166742600-166744000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:166742600-166744200	Weak transcription	Brain Hippocampus Middle	brain
48	chr6:166742600-166744200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr6:166742600-166744200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:166742600-166745600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links