Variant report

Variant	rs1565815
Chromosome Location	chr12:105161579-105161580
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105154675..105157648-chr12:105161416..105163979,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1002803	0.94[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs1038968	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10507184	1.00[CEU][hapmap];0.98[GIH][hapmap];0.94[TSI][hapmap]
rs1070316	0.82[CEU][hapmap]
rs10778358	0.89[GIH][hapmap]
rs1155994	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1316594	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1389609	0.96[EUR][1000 genomes]
rs1389610	0.82[EUR][1000 genomes]
rs1389612	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1474459	0.89[CEU][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs1565813	0.94[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs2047124	0.92[EUR][1000 genomes]
rs2088019	0.83[EUR][1000 genomes]
rs2131806	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs2141248	0.91[EUR][1000 genomes]
rs2245927	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2245929	0.84[EUR][1000 genomes]
rs2245931	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2248012	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2249454	0.87[GIH][hapmap]
rs2453154	0.94[CEU][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs2453155	0.94[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.81[MEX][hapmap];0.82[EUR][1000 genomes]
rs2453156	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2453157	0.96[EUR][1000 genomes]
rs2453158	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2453160	0.91[EUR][1000 genomes]
rs2453161	0.89[CEU][hapmap];0.80[GIH][hapmap];0.83[EUR][1000 genomes]
rs2453166	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs2453167	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2453168	0.96[EUR][1000 genomes]
rs2463016	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463017	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463018	0.89[CEU][hapmap];0.91[GIH][hapmap];0.80[TSI][hapmap];0.88[EUR][1000 genomes]
rs2463020	0.84[EUR][1000 genomes]
rs2463025	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463429	0.96[EUR][1000 genomes]
rs2463431	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463432	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463433	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2463434	0.84[EUR][1000 genomes]
rs2463435	0.83[EUR][1000 genomes]
rs2463437	0.94[CEU][hapmap];0.80[GIH][hapmap];0.82[EUR][1000 genomes]
rs2463438	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2463439	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs2463440	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs2463441	0.89[CEU][hapmap];0.80[GIH][hapmap]
rs2463442	0.84[CEU][hapmap]
rs2463443	0.84[CEU][hapmap]
rs2463444	0.84[CEU][hapmap]
rs2468082	0.84[EUR][1000 genomes]
rs2468083	0.96[EUR][1000 genomes]
rs2468089	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2468090	0.87[EUR][1000 genomes]
rs2468099	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2468100	0.93[EUR][1000 genomes]
rs2468105	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2468109	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2468110	0.89[CEU][hapmap];0.80[GIH][hapmap]
rs2468112	0.80[EUR][1000 genomes]
rs2468340	0.88[EUR][1000 genomes]
rs2565167	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2642109	0.81[EUR][1000 genomes]
rs2642110	0.96[EUR][1000 genomes]
rs2642116	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2730291	0.94[CEU][hapmap];0.91[GIH][hapmap];0.86[EUR][1000 genomes]
rs2730295	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2731030	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4393404	0.89[GIH][hapmap]
rs6539167	0.92[EUR][1000 genomes]
rs6539170	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs703681	0.89[CEU][hapmap];0.80[GIH][hapmap];0.81[EUR][1000 genomes]
rs7135015	0.89[GIH][hapmap]
rs7138686	0.84[GIH][hapmap]
rs7847	0.88[EUR][1000 genomes]
rs7980681	0.90[EUR][1000 genomes]
rs903247	0.94[CEU][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899496	chr12:105152391-105199038	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899497	chr12:105155291-105247010	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1565815	HCFC2	cis	parietal	SCAN
rs1565815	C20orf103	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105145600-105162800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:105151600-105161800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr12:105151600-105162800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:105152400-105162600	Weak transcription	Brain Anterior Caudate	brain
5	chr12:105153200-105161800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:105154400-105162800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:105156200-105163000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:105157400-105162600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:105157400-105162600	Weak transcription	NHEK	skin
10	chr12:105157400-105162800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:105157600-105162000	Weak transcription	HMEC	breast
12	chr12:105157600-105162200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:105158800-105161800	Weak transcription	Ovary	ovary
14	chr12:105160800-105163400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr12:105160800-105163400	Enhancers	Brain Germinal Matrix	brain
16	chr12:105161000-105163000	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:105161200-105161600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:105161200-105161800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:105161200-105163400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:105161200-105163400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr12:105161200-105163400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr12:105161400-105161600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:105161400-105161800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:105161400-105161800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr12:105161400-105162800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:105161400-105163400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr12:105161400-105163400	Enhancers	Fetal Brain Male	brain

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