Variant report

Variant	rs2185684
Chromosome Location	chr1:224647741-224647742
allele	G/T
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: 116 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10127813	0.86[EUR][1000 genomes]
rs10127953	0.86[EUR][1000 genomes]
rs10128058	0.86[EUR][1000 genomes]
rs10159333	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10495219	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10753465	0.86[EUR][1000 genomes]
rs10753466	0.86[EUR][1000 genomes]
rs10753467	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10753468	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10916606	0.85[EUR][1000 genomes]
rs10916607	0.86[EUR][1000 genomes]
rs10916614	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10916616	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10916617	0.99[EUR][1000 genomes]
rs10916619	0.99[EUR][1000 genomes]
rs11576835	0.86[EUR][1000 genomes]
rs11577170	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11577183	0.86[EUR][1000 genomes]
rs11578709	0.90[EUR][1000 genomes]
rs11579952	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584057	0.88[EUR][1000 genomes]
rs11584247	0.85[EUR][1000 genomes]
rs11584638	0.96[EUR][1000 genomes]
rs11584980	0.86[EUR][1000 genomes]
rs11586729	0.85[EUR][1000 genomes]
rs11588973	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590658	0.99[EUR][1000 genomes]
rs11800613	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801436	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11801645	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11803414	0.87[EUR][1000 genomes]
rs11803981	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11805973	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807763	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11807942	0.86[EUR][1000 genomes]
rs11811053	0.82[EUR][1000 genomes]
rs12062871	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12731035	0.88[EUR][1000 genomes]
rs12731630	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738799	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12739486	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12740255	0.86[EUR][1000 genomes]
rs12742821	0.86[EUR][1000 genomes]
rs12742989	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745610	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12747286	0.94[EUR][1000 genomes]
rs12751161	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12754832	0.86[EUR][1000 genomes]
rs12755338	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12755816	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12758302	0.92[EUR][1000 genomes]
rs12758579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12759275	0.86[EUR][1000 genomes]
rs1539207	0.86[EUR][1000 genomes]
rs1544196	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16848365	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17503938	0.86[EUR][1000 genomes]
rs17570292	0.89[EUR][1000 genomes]
rs28434172	0.94[EUR][1000 genomes]
rs2897048	0.94[EUR][1000 genomes]
rs34791963	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35011635	0.96[EUR][1000 genomes]
rs35031726	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35067427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35169600	0.84[EUR][1000 genomes]
rs35277713	0.96[EUR][1000 genomes]
rs35303987	0.96[EUR][1000 genomes]
rs35341841	0.83[EUR][1000 genomes]
rs35365551	0.92[EUR][1000 genomes]
rs35571080	0.99[EUR][1000 genomes]
rs35767322	0.92[EUR][1000 genomes]
rs35804313	0.90[EUR][1000 genomes]
rs35915186	0.95[EUR][1000 genomes]
rs35972228	0.83[EUR][1000 genomes]
rs36138926	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653587	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4654037	0.86[EUR][1000 genomes]
rs55730749	0.99[EUR][1000 genomes]
rs56223447	0.86[EUR][1000 genomes]
rs6426121	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426123	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426125	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426126	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs66467176	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66530931	0.80[EUR][1000 genomes]
rs6663522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671751	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.86[EUR][1000 genomes]
rs6691779	0.86[EUR][1000 genomes]
rs6693287	0.85[EUR][1000 genomes]
rs6698343	0.89[EUR][1000 genomes]
rs6701145	0.86[EUR][1000 genomes]
rs67065875	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs68037178	0.84[EUR][1000 genomes]
rs71644786	0.92[EUR][1000 genomes]
rs7365151	0.99[EUR][1000 genomes]
rs7512431	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7513208	0.86[EUR][1000 genomes]
rs7514284	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7514575	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7517754	0.86[EUR][1000 genomes]
rs7518109	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7519734	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7522956	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7527044	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7529067	0.86[EUR][1000 genomes]
rs7529310	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs867362	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs885606	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9970697	0.86[AMR][1000 genomes];0.99[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2185684	CNIH4	cis	Esophagus Mucosa	GTEx
rs2185684	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs2185684	CNIH4	cis	Adipose Subcutaneous	GTEx
rs2185684	CNIH4	cis	Heart Left Ventricle	GTEx
rs2185684	CNIH4	cis	Thyroid	GTEx
rs2185684	CNIH4	cis	Esophagus Muscularis	GTEx
rs2185684	CNIH4	cis	Muscle Skeletal	GTEx

Chromatin state (count:39 , 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	chr1:224645000-224649200	Weak transcription	Esophagus	oesophagus
13	chr1:224645000-224649200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:224645200-224647800	Enhancers	Adipose Nuclei	Adipose
15	chr1:224645400-224648400	Weak transcription	Fetal Stomach	stomach
16	chr1:224645400-224652000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:224645400-224653400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:224645400-224653400	Weak transcription	GM12878-XiMat	blood
19	chr1:224645400-224656200	Weak transcription	Primary T cells from cord blood	blood
20	chr1:224645800-224650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:224646000-224647800	Enhancers	Primary hematopoietic stem cells	blood
22	chr1:224646000-224647800	Enhancers	Brain Hippocampus Middle	brain
23	chr1:224646000-224648200	Enhancers	Stomach Mucosa	stomach
24	chr1:224646200-224647800	Enhancers	Ovary	ovary
25	chr1:224646400-224647800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:224646400-224647800	Enhancers	Fetal Intestine Large	intestine
27	chr1:224646400-224647800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr1:224646400-224648400	Enhancers	K562	blood
29	chr1:224646600-224647800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:224646600-224647800	Enhancers	Fetal Lung	lung
31	chr1:224646600-224648000	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr1:224646800-224647800	Enhancers	Primary B cells from peripheral blood	blood
33	chr1:224647200-224648000	Enhancers	Spleen	Spleen
34	chr1:224647400-224647800	Enhancers	Right Atrium	heart
35	chr1:224647400-224647800	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:224647600-224647800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:224647600-224647800	Enhancers	Liver	Liver
38	chr1:224647600-224647800	Enhancers	Lung	lung
39	chr1:224647600-224651400	Weak transcription	Fetal Brain Male	brain

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