Variant report

Variant	rs16827968
Chromosome Location	chr2:187380870-187380871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187378179..187380116-chr2:187380297..187381882,2	K562	blood:
2	chr2:187378645..187382692-chr2:187454130..187456514,4	MCF-7	breast:
3	chr2:187380709..187383265-chr2:187491364..187493572,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3H15-2	chr2:187380736-187381418	NONHSAT075998

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10177153	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10181681	0.90[EUR][1000 genomes]
rs10190003	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10198525	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10200749	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1037241	0.80[EUR][1000 genomes]
rs10497671	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10497672	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs11675633	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11675656	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11678950	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11680486	0.80[EUR][1000 genomes]
rs11690758	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693797	0.80[EUR][1000 genomes]
rs11888432	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11901465	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11903027	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13392819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13394241	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13401304	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13428033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1448848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1448849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1448855	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16827994	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1868383	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1869031	0.94[EUR][1000 genomes]
rs2084488	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084490	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2197139	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2370688	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2887826	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35642346	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55719959	0.80[EUR][1000 genomes]
rs56137171	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61226319	0.80[EUR][1000 genomes]
rs61434493	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434174	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6709401	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6716324	0.80[EUR][1000 genomes]
rs6717525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs6724161	0.85[AMR][1000 genomes]
rs6728382	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6731567	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[EUR][1000 genomes]
rs6744717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72895449	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72897386	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72901315	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72901322	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7579259	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7584137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603088	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9917285	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16827968	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187357400-187383000	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:187357600-187382600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:187357600-187386200	Strong transcription	Dnd41	blood
4	chr2:187358600-187385800	Weak transcription	Esophagus	oesophagus
5	chr2:187359600-187386400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:187359800-187381400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr2:187359800-187387200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:187360000-187386800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:187361200-187385600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:187361400-187389200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:187363000-187385600	Weak transcription	Aorta	Aorta
12	chr2:187363000-187387800	Weak transcription	Pancreas	Pancrea
13	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:187363200-187397600	Weak transcription	Small Intestine	intestine
15	chr2:187367200-187385600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:187367200-187396800	Weak transcription	Gastric	stomach
17	chr2:187367200-187405800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:187369200-187383400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:187370800-187385600	Weak transcription	Fetal Stomach	stomach
20	chr2:187370800-187385600	Weak transcription	Spleen	Spleen
21	chr2:187370800-187385800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr2:187370800-187385800	Weak transcription	Lung	lung
23	chr2:187370800-187386800	Weak transcription	Stomach Mucosa	stomach
24	chr2:187371000-187385800	Weak transcription	Thymus	Thymus
25	chr2:187371000-187389400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr2:187371000-187395800	Weak transcription	Fetal Heart	heart
27	chr2:187371000-187407800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:187371400-187385600	Weak transcription	Ovary	ovary
29	chr2:187372200-187390000	Weak transcription	Fetal Brain Male	brain
30	chr2:187373600-187385600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:187373600-187385600	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:187373600-187388000	Weak transcription	Psoas Muscle	Psoas
33	chr2:187373600-187395800	Weak transcription	HSMMtube	muscle
34	chr2:187373600-187397600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:187373800-187385800	Weak transcription	Brain Cingulate Gyrus	brain
36	chr2:187373800-187385800	Weak transcription	Left Ventricle	heart
37	chr2:187373800-187386000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:187373800-187387000	Weak transcription	Rectal Smooth Muscle	rectum
39	chr2:187373800-187387800	Weak transcription	Right Ventricle	heart
40	chr2:187373800-187390200	Weak transcription	Brain Anterior Caudate	brain
41	chr2:187374000-187381800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:187374000-187385800	Weak transcription	Fetal Brain Female	brain
43	chr2:187374000-187388600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr2:187374200-187381600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr2:187374200-187386400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:187374200-187386600	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:187374200-187386600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:187374400-187383000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:187374400-187386400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:187374400-187389800	Weak transcription	Brain Germinal Matrix	brain

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