Variant report

Variant	rs7519734
Chromosome Location	chr1:224549524-224549525
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224548342..224549997-chr1:226160381..226162583,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10127813	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10127953	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10128058	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10159333	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10495219	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10753465	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753466	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10753467	0.86[EUR][1000 genomes]
rs10753468	0.86[EUR][1000 genomes]
rs10799569	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916606	0.95[EUR][1000 genomes]
rs10916607	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916614	0.90[EUR][1000 genomes]
rs10916616	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10916617	0.86[EUR][1000 genomes]
rs10916619	0.86[EUR][1000 genomes]
rs11576835	0.96[EUR][1000 genomes]
rs11577170	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11577183	0.96[EUR][1000 genomes]
rs11579952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584247	0.96[EUR][1000 genomes]
rs11584638	0.88[EUR][1000 genomes]
rs11584980	0.96[EUR][1000 genomes]
rs11586729	0.96[EUR][1000 genomes]
rs11588973	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11590658	0.86[EUR][1000 genomes]
rs11800613	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11801436	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11801645	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11803414	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803981	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805973	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11807763	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11807942	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811053	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12062871	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12731035	0.94[EUR][1000 genomes]
rs12731630	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12738799	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12739486	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12740255	0.96[EUR][1000 genomes]
rs12742821	0.96[EUR][1000 genomes]
rs12742989	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12743200	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12745610	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12747286	0.90[EUR][1000 genomes]
rs12751161	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12754832	0.96[EUR][1000 genomes]
rs12755338	0.84[EUR][1000 genomes]
rs12755816	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12758302	0.83[EUR][1000 genomes]
rs12758579	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12759275	0.96[EUR][1000 genomes]
rs1539207	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1544196	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16848365	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17503938	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185684	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28434172	0.88[EUR][1000 genomes]
rs2897048	0.89[EUR][1000 genomes]
rs35011635	0.88[EUR][1000 genomes]
rs35031726	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35067427	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35169600	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35277713	0.88[EUR][1000 genomes]
rs35303987	0.88[EUR][1000 genomes]
rs35341841	0.94[EUR][1000 genomes]
rs35365551	0.84[EUR][1000 genomes]
rs35571080	0.86[EUR][1000 genomes]
rs35915186	0.82[EUR][1000 genomes]
rs35972228	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs36138926	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4653587	0.89[EUR][1000 genomes]
rs4654037	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55730749	0.86[EUR][1000 genomes]
rs56223447	0.96[EUR][1000 genomes]
rs6426121	0.94[EUR][1000 genomes]
rs6426123	0.89[EUR][1000 genomes]
rs6426125	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6426126	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66467176	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6663522	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6671751	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672859	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6675858	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691779	0.96[EUR][1000 genomes]
rs6693287	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6701145	0.96[EUR][1000 genomes]
rs67065875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68037178	0.95[EUR][1000 genomes]
rs7365151	0.86[EUR][1000 genomes]
rs7512431	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7513208	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514284	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7514575	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7517754	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518109	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7522956	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7527044	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7529067	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529310	0.89[EUR][1000 genomes]
rs867362	0.86[EUR][1000 genomes]
rs885606	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9970697	0.85[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	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7519734	CNIH4	cis	Thyroid	GTEx
rs7519734	CNIH4	cis	Adipose Subcutaneous	GTEx
rs7519734	CNIH4	cis	Stomach	GTEx
rs7519734	CNIH4	cis	Esophagus Mucosa	GTEx
rs7519734	CNIH4	cis	Muscle Skeletal	GTEx
rs7519734	CNIH4	cis	Nerve Tibial	GTEx
rs7519734	CNIH4	cis	Esophagus Muscularis	GTEx
rs7519734	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs7519734	CNIH4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
2	chr1:224545400-224553800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:224545600-224555200	Weak transcription	Lung	lung
5	chr1:224545600-224555200	Weak transcription	Ovary	ovary
6	chr1:224545800-224549800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:224545800-224555000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
10	chr1:224546000-224549800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr1:224546000-224551600	Weak transcription	Thymus	Thymus
12	chr1:224546000-224554600	Weak transcription	Liver	Liver
13	chr1:224546000-224555200	Weak transcription	Fetal Kidney	kidney
14	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:224546200-224550800	Weak transcription	Fetal Muscle Leg	muscle
18	chr1:224546200-224551000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:224546200-224551200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:224546200-224551400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:224546200-224551400	Weak transcription	HSMMtube	muscle
22	chr1:224546200-224551800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:224546200-224552800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:224546200-224553000	Weak transcription	HSMM	muscle
25	chr1:224546200-224553200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:224546200-224553400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:224546200-224553600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:224546200-224554800	Weak transcription	Placenta	Placenta
29	chr1:224546200-224554800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:224546200-224555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:224546200-224555200	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:224546200-224555200	Weak transcription	Brain Substantia Nigra	brain
33	chr1:224546200-224555200	Weak transcription	Colonic Mucosa	Colon
34	chr1:224546200-224555200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:224546200-224555200	Weak transcription	Right Ventricle	heart
36	chr1:224546200-224555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:224546400-224551400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:224546400-224551600	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:224546400-224552800	Weak transcription	Osteobl	bone
40	chr1:224546400-224553000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:224546400-224553000	Weak transcription	Fetal Lung	lung
42	chr1:224546400-224553000	Weak transcription	Fetal Thymus	thymus
43	chr1:224546400-224553200	Weak transcription	NH-A	brain
44	chr1:224546400-224555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr1:224546400-224555200	Weak transcription	Left Ventricle	heart
46	chr1:224546400-224555400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr1:224546800-224549800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:224546800-224550400	Weak transcription	GM12878-XiMat	blood
49	chr1:224546800-224550800	Weak transcription	HUVEC	blood vessel
50	chr1:224546800-224551200	Weak transcription	Primary B cells from cord blood	blood

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