Variant report

Variant	rs10495219
Chromosome Location	chr1:224606249-224606250
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224604661..224609524-chr1:224620120..224624801,9	MCF-7	breast:
2	chr1:224595004..224596638-chr1:224604243..224607134,2	K562	blood:
3	chr1:224602276..224606277-chr1:224608631..224611582,5	MCF-7	breast:
4	chr1:224595604..224598812-chr1:224605790..224608888,3	MCF-7	breast:
5	chr1:224604963..224607322-chr1:224610128..224612873,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162923	Chromatin interaction
ENSG00000143786	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs10127813	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10127953	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10128058	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10159333	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753465	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10753466	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753467	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753468	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10799569	0.90[EUR][1000 genomes]
rs10916606	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916607	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10916614	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916616	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916617	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10916619	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11576835	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11577170	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11577183	0.90[EUR][1000 genomes]
rs11578709	0.86[EUR][1000 genomes]
rs11579952	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11584057	0.84[EUR][1000 genomes]
rs11584247	0.89[EUR][1000 genomes]
rs11584638	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11584980	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11586729	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11588973	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11590658	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs11800613	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11801436	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801645	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803414	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs11803981	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11805973	0.95[CEU][hapmap];0.97[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807763	1.00[CEU][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807942	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11811053	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12062871	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12731035	0.92[EUR][1000 genomes]
rs12731630	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12738799	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12739486	1.00[CEU][hapmap];0.97[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12740255	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs12742821	0.90[EUR][1000 genomes]
rs12742989	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12743200	1.00[CEU][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12745610	1.00[CEU][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12747286	0.98[EUR][1000 genomes]
rs12751161	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12754832	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs12755338	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12755816	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12758302	0.93[EUR][1000 genomes]
rs12758579	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12759275	0.90[EUR][1000 genomes]
rs1539207	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1544196	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16848365	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]
rs17503938	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs17570292	0.85[EUR][1000 genomes]
rs2185684	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28434172	0.98[EUR][1000 genomes]
rs2897048	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs34791963	0.88[AMR][1000 genomes]
rs35011635	0.97[EUR][1000 genomes]
rs35031726	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35067427	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35169600	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35277713	0.98[EUR][1000 genomes]
rs35303987	0.98[EUR][1000 genomes]
rs35341841	0.87[EUR][1000 genomes]
rs35365551	0.94[EUR][1000 genomes]
rs35571080	0.95[EUR][1000 genomes]
rs35767322	0.88[EUR][1000 genomes]
rs35804313	0.86[EUR][1000 genomes]
rs35915186	0.91[EUR][1000 genomes]
rs35972228	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36138926	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4653585	1.00[CEU][hapmap]
rs4653587	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654037	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs55730749	0.95[EUR][1000 genomes]
rs56223447	0.90[EUR][1000 genomes]
rs6426121	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426123	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426125	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6426126	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467176	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6663522	1.00[CEU][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6671751	0.95[CEU][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6672859	0.90[EUR][1000 genomes]
rs6675858	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6691779	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs6693287	1.00[CEU][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6698343	0.85[EUR][1000 genomes]
rs6701145	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs67065875	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs68037178	0.88[EUR][1000 genomes]
rs71644786	0.88[EUR][1000 genomes]
rs7365151	0.95[EUR][1000 genomes]
rs7512431	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513208	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7514284	0.91[CEU][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514575	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517754	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs7518109	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7519734	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7522956	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527044	1.00[CEU][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7529067	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7529310	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867362	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885606	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970697	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
4	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
5	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
6	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
7	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
rs10495219	CNIH4	cis	Adipose Subcutaneous	GTEx
rs10495219	CNIH4	cis	Stomach	GTEx
rs10495219	CNIH4	cis	Thyroid	GTEx
rs10495219	CNIH4	cis	Muscle Skeletal	GTEx
rs10495219	CNIH4	cis	Esophagus Muscularis	GTEx
rs10495219	CNIH4	cis	Esophagus Mucosa	GTEx
rs10495219	CNIH4	cis	Nerve Tibial	GTEx
rs10495219	CNIH4	cis	Skin Sun Exposed Lower leg	GTEx
rs10495219	CNIH4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:224572000-224617800	Strong transcription	Fetal Thymus	thymus
3	chr1:224572400-224617600	Strong transcription	Placenta	Placenta
4	chr1:224572600-224617600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:224572600-224617600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:224572600-224618400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr1:224573200-224618400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:224573200-224618400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:224573600-224614200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:224573600-224618200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:224573800-224615200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:224574000-224613600	Strong transcription	Adipose Nuclei	Adipose
13	chr1:224574600-224613600	Strong transcription	Duodenum Mucosa	Duodenum
14	chr1:224575000-224607600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:224575200-224607600	Strong transcription	Fetal Intestine Large	intestine
16	chr1:224575200-224613800	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr1:224575200-224616600	Strong transcription	Dnd41	blood
18	chr1:224575200-224616800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:224576200-224614000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:224576400-224614600	Strong transcription	HSMM	muscle
21	chr1:224577000-224617400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:224578800-224614000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:224578800-224617200	Strong transcription	Liver	Liver
24	chr1:224579600-224617400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:224579800-224616000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:224581800-224615800	Strong transcription	K562	blood
27	chr1:224589000-224611200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:224590400-224612600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:224591200-224613000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:224591400-224607800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:224593400-224617000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:224593800-224613600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:224595400-224613400	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:224595400-224618000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:224595600-224613200	Strong transcription	HUVEC	blood vessel
36	chr1:224596000-224608800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr1:224596200-224614400	Strong transcription	NHDF-Ad	bronchial
38	chr1:224596200-224614600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:224596200-224615400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:224596600-224611600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:224596600-224614200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:224596600-224614600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:224596800-224614200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:224597200-224607800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:224597200-224613600	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr1:224597600-224612200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:224597600-224616200	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:224598200-224617000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:224598400-224612400	Strong transcription	Brain Substantia Nigra	brain
50	chr1:224598800-224609000	Weak transcription	Esophagus	oesophagus

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