Variant report

Variant	rs16848365
Chromosome Location	chr1:224637381-224637382
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224627143..224628933-chr1:224633589..224638837,4	MCF-7	breast:
2	chr1:224637202..224641034-chr1:224641889..224644811,3	K562	blood:
3	chr1:224636445..224639746-chr1:224642433..224645284,3	K562	blood:
4	chr1:224634502..224636379-chr1:224636698..224640995,4	K562	blood:
5	chr1:224615678..224629188-chr1:224635437..224647951,56	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10127813	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10127953	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10128058	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10159333	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10916606	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11577170	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11577183	0.86[EUR][1000 genomes]
rs11578709	0.90[EUR][1000 genomes]
rs11579952	0.95[CEU][hapmap];0.97[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11584057	0.88[EUR][1000 genomes]
rs11584247	0.85[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11584980	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11588973	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11801436	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs11803981	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11805973	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807763	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11811053	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12062871	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12731035	0.88[EUR][1000 genomes]
rs12731630	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs12742821	0.86[EUR][1000 genomes]
rs12742989	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12745610	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12747286	0.94[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12755338	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12755816	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.92[EUR][1000 genomes]
rs12758579	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12759275	0.86[EUR][1000 genomes]
rs1539207	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503938	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs17570292	0.89[EUR][1000 genomes]
rs2185684	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28434172	0.94[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs34791963	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35011635	0.96[EUR][1000 genomes]
rs35031726	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35067427	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35169600	0.82[AMR][1000 genomes];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	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654037	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs55730749	0.99[EUR][1000 genomes]
rs56223447	0.86[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426123	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6426126	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs66530931	0.80[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6671751	0.95[CEU][hapmap];0.97[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6691779	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.97[YRI][hapmap];0.85[EUR][1000 genomes]
rs6698343	0.89[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs67065875	0.83[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	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7514284	0.90[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs7518109	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7522956	1.00[CEU][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7529310	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv1013149	chr1:224605943-224646382	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv535312	chr1:224605943-224646382	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs16848365	CNIH4	cis	Adipose Subcutaneous	GTEx
rs16848365	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs16848365	CNIH4	cis	Esophagus Mucosa	GTEx
rs16848365	CNIH4	cis	Muscle Skeletal	GTEx
rs16848365	CNIH4	cis	Heart Left Ventricle	GTEx
rs16848365	CNIH4	cis	Thyroid	GTEx
rs16848365	CNIH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224623200-224644400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:224623400-224638000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr1:224623400-224641000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:224623400-224643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:224623400-224644600	Weak transcription	Right Ventricle	heart
6	chr1:224623600-224637400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr1:224623600-224642200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:224623600-224644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:224623600-224644600	Weak transcription	Brain Substantia Nigra	brain
10	chr1:224623800-224644400	Weak transcription	Brain Anterior Caudate	brain
11	chr1:224624000-224637600	Weak transcription	Fetal Thymus	thymus
12	chr1:224624000-224642200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:224624000-224644000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:224624000-224644600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:224624000-224644600	Weak transcription	Brain Angular Gyrus	brain
16	chr1:224624000-224645000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:224624000-224645000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:224624000-224645000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:224624000-224646800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr1:224624200-224642200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:224624400-224637600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:224624800-224637800	Weak transcription	Dnd41	blood
23	chr1:224624800-224638200	Weak transcription	Fetal Muscle Leg	muscle
24	chr1:224624800-224641400	Weak transcription	Fetal Intestine Small	intestine
25	chr1:224624800-224644000	Weak transcription	Pancreas	Pancrea
26	chr1:224624800-224644400	Weak transcription	A549	lung
27	chr1:224624800-224645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr1:224625000-224637600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:224625200-224637800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:224625200-224644600	Weak transcription	GM12878-XiMat	blood
31	chr1:224625200-224645000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:224625400-224637400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:224627000-224644000	Weak transcription	Placenta	Placenta
34	chr1:224627200-224641000	Weak transcription	HepG2	liver
35	chr1:224627200-224642000	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:224627200-224644400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:224628200-224645000	Weak transcription	Thymus	Thymus
38	chr1:224628400-224641400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:224628400-224644600	Weak transcription	Fetal Lung	lung
40	chr1:224628400-224644800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr1:224628400-224648800	Weak transcription	Fetal Brain Female	brain
42	chr1:224628600-224644200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:224628800-224643800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:224629200-224644200	Weak transcription	Brain Germinal Matrix	brain
46	chr1:224629200-224644600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:224630600-224641600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr1:224630600-224641600	Weak transcription	K562	blood
49	chr1:224630800-224643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:224630800-224644600	Weak transcription	Primary T cells fromperipheralblood	blood

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