Variant report

Variant	rs55697950
Chromosome Location	chr7:56141283-56141284
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:56140513-56143098	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:56119174..56121015-chr7:56139907..56143557,3	MCF-7	breast:
2	chr7:56139442..56142282-chr7:56145954..56148779,2	MCF-7	breast:
3	chr7:56140520..56143096-chr7:56151808..56154646,2	K562	blood:
4	chr7:56031348..56032996-chr7:56140272..56142339,2	K562	blood:
5	chr7:56139457..56142087-chr7:56158811..56160685,2	MCF-7	breast:

No data

Variant related genes	Relation type
SUMF2	TF binding region
ENSG00000164776	Chromatin interaction
ENSG00000146731	Chromatin interaction
ENSG00000146733	Chromatin interaction
ENSG00000146729	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10043	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1064337	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11238392	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238393	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11238395	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11764629	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11765364	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11772545	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12535749	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535872	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12538444	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1894833	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894834	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2002693	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2080141	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2538048	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908546	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908547	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2908548	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2965455	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55863006	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56389944	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457279	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457281	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457282	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457284	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62457286	0.82[ASN][1000 genomes]
rs62457287	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457288	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457289	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62457291	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6951202	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6955663	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6965614	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73140771	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7801405	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7808729	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7811889	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816407	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs816410	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8406	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9649860	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829874	chr7:55382925-56369816	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv995105	chr7:55606107-56174888	Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers 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 miRNA target site	76 gene(s)	inside rSNPs	diseases
3	esv12412	chr7:55619800-56385412	Strong transcription Flanking Active TSS Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv949574	chr7:55705566-56544711	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	esv3446617	chr7:55745934-56485903	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
6	nsv529162	chr7:55800753-56174888	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	esv2761334	chr7:55823581-56424739	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
8	nsv1018806	chr7:55844931-56383936	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv538860	chr7:55844931-56383936	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv498114	chr7:55872850-56174888	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55697950	LOC146325	trans	lymphoblastoid	RTeQTL
rs55697950	CHCHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56131800-56146800	Weak transcription	Fetal Heart	heart
2	chr7:56132400-56141800	Weak transcription	Stomach Mucosa	stomach
3	chr7:56132400-56145400	Weak transcription	Spleen	Spleen
4	chr7:56133200-56141800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr7:56133200-56141800	Weak transcription	HepG2	liver
6	chr7:56133200-56142000	Weak transcription	Esophagus	oesophagus
7	chr7:56133200-56142200	Weak transcription	Right Atrium	heart
8	chr7:56133200-56145600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:56133200-56146400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr7:56133200-56147000	Weak transcription	Fetal Brain Male	brain
11	chr7:56133200-56147000	Weak transcription	Psoas Muscle	Psoas
12	chr7:56133400-56144200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:56133400-56145800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr7:56133600-56141800	Weak transcription	HUVEC	blood vessel
15	chr7:56133600-56144200	Weak transcription	NHDF-Ad	bronchial
16	chr7:56133600-56145400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:56133800-56141800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:56133800-56142000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:56133800-56143200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:56134000-56141800	Weak transcription	NHLF	lung
21	chr7:56134000-56152000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:56134000-56167800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr7:56134200-56167600	Weak transcription	Small Intestine	intestine
24	chr7:56135000-56141600	Strong transcription	Fetal Muscle Leg	muscle
25	chr7:56135000-56141800	Strong transcription	Fetal Intestine Small	intestine
26	chr7:56135000-56142600	Strong transcription	Fetal Stomach	stomach
27	chr7:56135800-56141800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:56136000-56141400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:56136000-56142200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr7:56136200-56141600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr7:56136200-56142000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr7:56136200-56142000	Strong transcription	Fetal Brain Female	brain
33	chr7:56137000-56141600	Weak transcription	K562	blood
34	chr7:56137200-56146000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:56137600-56141800	Weak transcription	Pancreas	Pancrea
36	chr7:56138200-56144200	Weak transcription	Hela-S3	cervix
37	chr7:56138600-56142000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:56138600-56144200	Weak transcription	Fetal Lung	lung
39	chr7:56138600-56144200	Weak transcription	Right Ventricle	heart
40	chr7:56138800-56141600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr7:56138800-56141800	Weak transcription	Brain Substantia Nigra	brain
42	chr7:56138800-56142200	Weak transcription	Left Ventricle	heart
43	chr7:56138800-56142400	Weak transcription	Osteobl	bone
44	chr7:56138800-56146800	Weak transcription	Aorta	Aorta
45	chr7:56138800-56146800	Weak transcription	HSMMtube	muscle
46	chr7:56138800-56156200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:56138800-56167600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr7:56139000-56141400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr7:56139000-56141800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr7:56139000-56141800	Weak transcription	Placenta	Placenta

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