Variant report

Variant	rs10916619
Chromosome Location	chr1:224644885-224644886
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224619496..224626224-chr1:224640836..224649586,12	K562	blood:
2	chr1:224633064..224636103-chr1:224643208..224646617,3	K562	blood:
3	chr1:224629495..224631561-chr1:224643787..224646406,3	K562	blood:
4	chr1:224607158..224609951-chr1:224643885..224645714,2	K562	blood:
5	chr1:224615678..224629188-chr1:224635437..224647951,56	MCF-7	breast:
6	chr1:224644724..224648422-chr1:224649777..224653927,3	K562	blood:
7	chr1:224625596..224628052-chr1:224644353..224645962,2	MCF-7	breast:
8	chr1:224643383..224644923-chr1:224691038..224692842,2	MCF-7	breast:
9	chr1:224617260..224625232-chr1:224640385..224647515,27	MCF-7	breast:
10	chr1:224636445..224639746-chr1:224642433..224645284,3	K562	blood:
11	chr1:224641326..224643104-chr1:224643904..224646218,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224644440-224644974	NONHSAT009806

No data

Variant related genes	Relation type
ENSG00000143786	Chromatin interaction
ENSG00000162923	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10127813	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10127953	0.86[EUR][1000 genomes]
rs10128058	0.86[EUR][1000 genomes]
rs10159333	0.96[EUR][1000 genomes]
rs10495219	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10753465	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs10753468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs10799569	0.86[EUR][1000 genomes]
rs10916606	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10916616	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs10916617	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];1.00[YRI][hapmap];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	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs11584057	0.87[EUR][1000 genomes]
rs11584247	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11584980	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11586729	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11588973	0.99[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800613	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs11801436	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11803414	0.94[CEU][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11803981	0.86[EUR][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11807763	1.00[CEU][hapmap];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	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12740255	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs12745610	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12747286	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12754832	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12755338	0.96[EUR][1000 genomes]
rs12755816	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];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	0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1539207	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs16848365	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs17503938	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];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]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.96[EUR][1000 genomes]
rs4654037	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs55730749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56223447	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6426123	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6426125	0.96[EUR][1000 genomes]
rs6426126	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs66467176	0.99[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[EUR][1000 genomes]
rs6671751	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs6672859	0.86[EUR][1000 genomes]
rs6675858	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6691779	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6698343	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6701145	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];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	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7514284	0.91[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7514575	0.94[EUR][1000 genomes]
rs7517754	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7518109	0.86[EUR][1000 genomes]
rs7519734	0.86[EUR][1000 genomes]
rs7522956	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7529067	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs7529310	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs867362	1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes]
rs885606	0.99[EUR][1000 genomes]
rs9970697	0.98[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs10916619	CNIH4	cis	Heart Left Ventricle	GTEx
rs10916619	CNIH4	cis	Liver	GTEx
rs10916619	CNIH4	cis	multi-tissue	Pritchard
rs10916619	CNIH4	trans	multi-tissue	Pritchard
rs10916619	CNIH4	cis	parietal	SCAN
rs10916619	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs10916619	CNIH4	cis	Muscle Skeletal	GTEx
rs10916619	CNIH4	cis	Esophagus Muscularis	GTEx
rs10916619	CNIH4	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224624000-224645000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:224624000-224645000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:224624000-224645000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:224624000-224646800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:224624800-224645000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:224625200-224645000	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:224628200-224645000	Weak transcription	Thymus	Thymus
8	chr1:224628400-224648800	Weak transcription	Fetal Brain Female	brain
9	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:224639000-224648400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:224641000-224645000	Enhancers	Fetal Intestine Large	intestine
12	chr1:224641800-224645200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:224642000-224646400	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:224642400-224645400	Enhancers	HMEC	breast
15	chr1:224643000-224645000	Enhancers	Esophagus	oesophagus
16	chr1:224643000-224646000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:224643400-224645000	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr1:224643400-224649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:224643600-224646600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:224643800-224645000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:224643800-224645000	Enhancers	Lung	lung
22	chr1:224643800-224645400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr1:224643800-224645400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:224643800-224646000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:224644000-224645000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:224644000-224645000	Enhancers	Duodenum Mucosa	Duodenum
27	chr1:224644000-224645200	Enhancers	Ovary	ovary
28	chr1:224644000-224645400	Enhancers	Brain Hippocampus Middle	brain
29	chr1:224644000-224645400	Enhancers	Placenta	Placenta
30	chr1:224644000-224645400	Enhancers	Pancreas	Pancrea
31	chr1:224644200-224645000	Enhancers	Fetal Muscle Trunk	muscle
32	chr1:224644200-224645200	Enhancers	Right Atrium	heart
33	chr1:224644200-224645400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr1:224644200-224647800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:224644400-224645000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:224644400-224645000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:224644400-224645000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:224644400-224645000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr1:224644400-224645000	Enhancers	HepG2	liver
40	chr1:224644400-224645000	Enhancers	K562	blood
41	chr1:224644400-224645200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:224644400-224645200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:224644400-224645200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr1:224644400-224645200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:224644400-224645200	Enhancers	Left Ventricle	heart
46	chr1:224644400-224645200	Enhancers	Psoas Muscle	Psoas
47	chr1:224644400-224645200	Enhancers	HSMM	muscle
48	chr1:224644400-224645200	Enhancers	NHDF-Ad	bronchial
49	chr1:224644400-224645400	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr1:224644400-224645400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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