Variant report

Variant	rs10196955
Chromosome Location	chr2:187320492-187320493
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	chr2:187314908..187317613-chr2:187318535..187320583,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3H15-1	chr2:187319228-187321649	NONHSAT075995

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10169008	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10169206	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10177153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10190003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10205170	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10208643	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497671	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931240	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11675633	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11688988	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11690758	0.89[ASN][1000 genomes]
rs11692347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11888880	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11888881	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11901465	0.89[ASN][1000 genomes]
rs11903027	0.89[ASN][1000 genomes]
rs12328822	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13397188	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398352	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13401304	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13414850	0.89[ASN][1000 genomes]
rs13428033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1448848	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1448849	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs1448855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1448857	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16827968	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1868383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2084488	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2084489	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084490	0.84[ASN][1000 genomes]
rs2197139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2370688	0.89[ASN][1000 genomes]
rs2887826	0.89[ASN][1000 genomes]
rs34234405	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35642346	0.89[ASN][1000 genomes]
rs56137171	0.89[ASN][1000 genomes]
rs61434493	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6434174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6709401	1.00[CHB][hapmap];0.83[MEX][hapmap]
rs6710436	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6715493	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717505	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717525	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6721789	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728382	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6728400	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6731567	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs6744717	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72895449	0.89[ASN][1000 genomes]
rs72897386	0.81[AMR][1000 genomes]
rs7579259	0.89[ASN][1000 genomes]
rs7582412	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7584137	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7585905	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597954	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606920	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9288129	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917285	0.81[AMR][1000 genomes];0.89[ASN][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	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005680	chr2:187244500-187320653	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536080	chr2:187244500-187320653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1001927	chr2:187264940-187325667	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv997835	chr2:187265730-187327561	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv536081	chr2:187265730-187327561	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10196955	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187293800-187322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:187297800-187331200	Weak transcription	Left Ventricle	heart
3	chr2:187299600-187322800	Weak transcription	Aorta	Aorta
4	chr2:187301400-187321000	Weak transcription	Primary T cells from cord blood	blood
5	chr2:187301400-187322600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr2:187301600-187322600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:187302200-187323200	Weak transcription	Ovary	ovary
8	chr2:187302600-187321200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:187303800-187323000	Weak transcription	Primary B cells from cord blood	blood
10	chr2:187304600-187322800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:187308000-187323800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr2:187308400-187322800	Weak transcription	Fetal Intestine Large	intestine
13	chr2:187308800-187323000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:187309000-187321800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:187309400-187322600	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:187313400-187322800	Weak transcription	Psoas Muscle	Psoas
17	chr2:187313600-187327000	Weak transcription	Pancreas	Pancrea
18	chr2:187315200-187322800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:187315600-187330800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:187315800-187322800	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:187316200-187322800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:187316400-187321400	Weak transcription	Brain Anterior Caudate	brain
23	chr2:187317000-187323000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:187317200-187322400	Weak transcription	Spleen	Spleen
25	chr2:187317800-187323000	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:187318000-187322800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:187318200-187321200	Weak transcription	HMEC	breast
28	chr2:187318200-187321400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:187318200-187322800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:187318200-187323200	Weak transcription	Fetal Kidney	kidney
31	chr2:187318600-187320800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr2:187318600-187321400	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:187318600-187321400	Strong transcription	HepG2	liver
34	chr2:187318800-187320800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr2:187318800-187320800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr2:187319400-187321400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:187319400-187322800	Weak transcription	Fetal Intestine Small	intestine
38	chr2:187319600-187320600	Strong transcription	Adipose Nuclei	Adipose
39	chr2:187319600-187320600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:187319600-187320800	Strong transcription	Liver	Liver
41	chr2:187319600-187321400	Strong transcription	Primary hematopoietic stem cells	blood
42	chr2:187319600-187323000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:187319800-187323000	Weak transcription	HSMM	muscle
44	chr2:187320200-187322000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:187320400-187321400	Strong transcription	Dnd41	blood

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