Variant report

Variant	rs55730749
Chromosome Location	chr1:224647569-224647570
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224644893..224646924-chr1:224647544..224649417,2	K562	blood:
2	chr1:224619496..224626224-chr1:224640836..224649586,12	K562	blood:
3	chr1:224645408..224648550-chr1:224650858..224654034,4	K562	blood:
4	chr1:224615678..224629188-chr1:224635437..224647951,56	MCF-7	breast:
5	chr1:224644724..224648422-chr1:224649777..224653927,3	K562	blood:
6	chr1:224645897..224648212-chr1:224688548..224690344,2	K562	blood:
7	chr1:224640725..224643210-chr1:224646698..224648571,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224646906-224648396	NONHSAT009808

No data

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10127813	0.86[EUR][1000 genomes]
rs10127953	0.86[EUR][1000 genomes]
rs10128058	0.86[EUR][1000 genomes]
rs10159333	0.96[EUR][1000 genomes]
rs10495219	0.95[EUR][1000 genomes]
rs10753465	0.86[EUR][1000 genomes]
rs10753466	0.86[EUR][1000 genomes]
rs10753467	0.99[EUR][1000 genomes]
rs10753468	0.99[EUR][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10916606	0.85[EUR][1000 genomes]
rs10916607	0.85[EUR][1000 genomes]
rs10916614	0.94[EUR][1000 genomes]
rs10916616	0.96[EUR][1000 genomes]
rs10916617	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10916619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11576835	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11577170	0.99[EUR][1000 genomes]
rs11577183	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11578709	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11579952	0.86[EUR][1000 genomes]
rs11584057	0.87[EUR][1000 genomes]
rs11584247	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11584638	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584980	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11586729	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11588973	0.99[EUR][1000 genomes]
rs11590658	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800613	0.99[EUR][1000 genomes]
rs11801436	0.88[EUR][1000 genomes]
rs11801645	0.88[EUR][1000 genomes]
rs11803414	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11803981	0.86[EUR][1000 genomes]
rs11805973	0.92[EUR][1000 genomes]
rs11807763	0.95[EUR][1000 genomes]
rs11807942	0.85[EUR][1000 genomes]
rs11811053	0.82[EUR][1000 genomes]
rs12062871	0.98[EUR][1000 genomes]
rs12731035	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12731630	0.99[EUR][1000 genomes]
rs12738799	0.95[EUR][1000 genomes]
rs12739486	0.95[EUR][1000 genomes]
rs12740255	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12742821	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12742989	0.96[EUR][1000 genomes]
rs12743200	0.99[EUR][1000 genomes]
rs12745610	0.86[EUR][1000 genomes]
rs12747286	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12751161	0.95[EUR][1000 genomes]
rs12754832	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12755338	0.96[EUR][1000 genomes]
rs12755816	0.86[EUR][1000 genomes]
rs12758302	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12758579	0.99[EUR][1000 genomes]
rs12759275	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1539207	0.86[EUR][1000 genomes]
rs1544196	0.98[EUR][1000 genomes]
rs16848365	0.99[EUR][1000 genomes]
rs17503938	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17570292	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2185684	0.99[EUR][1000 genomes]
rs28434172	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2897048	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34791963	0.82[EUR][1000 genomes]
rs35011635	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35031726	0.86[EUR][1000 genomes]
rs35067427	0.99[EUR][1000 genomes]
rs35169600	0.84[EUR][1000 genomes]
rs35277713	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35303987	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35341841	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35365551	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35571080	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35767322	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35804313	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35915186	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35972228	0.82[EUR][1000 genomes]
rs36138926	0.86[EUR][1000 genomes]
rs4653587	0.96[EUR][1000 genomes]
rs4654037	0.86[EUR][1000 genomes]
rs56223447	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426121	0.88[EUR][1000 genomes]
rs6426123	0.96[EUR][1000 genomes]
rs6426125	0.96[EUR][1000 genomes]
rs6426126	0.96[EUR][1000 genomes]
rs66467176	0.99[EUR][1000 genomes]
rs6663522	0.99[EUR][1000 genomes]
rs6671751	0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6691779	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693287	0.84[EUR][1000 genomes]
rs6698343	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6701145	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67065875	0.86[EUR][1000 genomes]
rs68037178	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71644786	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7365151	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512431	0.86[EUR][1000 genomes]
rs7513208	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7514284	0.88[EUR][1000 genomes]
rs7514575	0.94[EUR][1000 genomes]
rs7517754	0.86[EUR][1000 genomes]
rs7518109	0.86[EUR][1000 genomes]
rs7519734	0.86[EUR][1000 genomes]
rs7522956	0.86[EUR][1000 genomes]
rs7527044	0.94[EUR][1000 genomes]
rs7529067	0.86[EUR][1000 genomes]
rs7529310	0.96[EUR][1000 genomes]
rs867362	0.99[EUR][1000 genomes]
rs885606	0.99[EUR][1000 genomes]
rs9970697	0.98[EUR][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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55730749	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs55730749	CNIH4	cis	Thyroid	GTEx
rs55730749	CNIH4	cis	Esophagus Muscularis	GTEx
rs55730749	CNIH4	cis	Muscle Skeletal	GTEx
rs55730749	CNIH4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224628400-224648800	Weak transcription	Fetal Brain Female	brain
2	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:224639000-224648400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:224643400-224649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:224644200-224647800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:224644400-224648000	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr1:224644600-224647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:224644800-224647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:224644800-224647800	Enhancers	Fetal Intestine Small	intestine
10	chr1:224644800-224648200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:224644800-224651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:224645000-224647600	Weak transcription	Lung	lung
13	chr1:224645000-224649200	Weak transcription	Esophagus	oesophagus
14	chr1:224645000-224649200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:224645200-224647600	Enhancers	Brain Angular Gyrus	brain
16	chr1:224645200-224647800	Enhancers	Adipose Nuclei	Adipose
17	chr1:224645400-224647600	Weak transcription	Liver	Liver
18	chr1:224645400-224647600	Enhancers	Colon Smooth Muscle	Colon
19	chr1:224645400-224648400	Weak transcription	Fetal Stomach	stomach
20	chr1:224645400-224652000	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:224645400-224653400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:224645400-224653400	Weak transcription	GM12878-XiMat	blood
23	chr1:224645400-224656200	Weak transcription	Primary T cells from cord blood	blood
24	chr1:224645800-224650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:224646000-224647800	Enhancers	Primary hematopoietic stem cells	blood
26	chr1:224646000-224647800	Enhancers	Brain Hippocampus Middle	brain
27	chr1:224646000-224648200	Enhancers	Stomach Mucosa	stomach
28	chr1:224646200-224647600	Enhancers	Brain Cingulate Gyrus	brain
29	chr1:224646200-224647800	Enhancers	Ovary	ovary
30	chr1:224646400-224647600	Enhancers	HUVEC	blood vessel
31	chr1:224646400-224647800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:224646400-224647800	Enhancers	Fetal Intestine Large	intestine
33	chr1:224646400-224647800	Enhancers	Rectal Mucosa Donor 29	rectum
34	chr1:224646400-224648400	Enhancers	K562	blood
35	chr1:224646600-224647600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:224646600-224647600	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:224646600-224647600	Enhancers	Brain Substantia Nigra	brain
38	chr1:224646600-224647800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr1:224646600-224647800	Enhancers	Fetal Lung	lung
40	chr1:224646600-224648000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr1:224646800-224647600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr1:224646800-224647800	Enhancers	Primary B cells from peripheral blood	blood
43	chr1:224647000-224647600	Enhancers	Fetal Brain Male	brain
44	chr1:224647200-224647600	Enhancers	Fetal Thymus	thymus
45	chr1:224647200-224648000	Enhancers	Spleen	Spleen
46	chr1:224647400-224647600	Enhancers	Colonic Mucosa	Colon
47	chr1:224647400-224647600	Enhancers	Left Ventricle	heart
48	chr1:224647400-224647800	Enhancers	Right Atrium	heart
49	chr1:224647400-224647800	Enhancers	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links