Variant report

Variant	rs2274985
Chromosome Location	chr1:10573867-10573868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10533965..10535483-chr1:10572998..10574939,2	K562	blood:
2	chr1:10573337..10575488-chr1:10723481..10725688,2	K562	blood:
3	chr1:10566008..10570273-chr1:10573569..10578315,6	K562	blood:
4	chr1:10569482..10571483-chr1:10572910..10575292,2	MCF-7	breast:
5	chr1:10571375..10572978-chr1:10573706..10575534,2	K562	blood:
6	chr1:10545220..10547716-chr1:10573359..10575513,2	K562	blood:

Variant related genes	Relation type
ENSG00000142655	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10779737	0.88[EUR][1000 genomes]
rs11121579	0.81[CEU][hapmap]
rs11121581	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11580264	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11584327	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[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12073943	0.89[EUR][1000 genomes]
rs12117392	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12120962	1.00[LWK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12127400	1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs12565133	0.86[TSI][hapmap]
rs17035189	0.88[CEU][hapmap];1.00[GIH][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1755592	0.90[EUR][1000 genomes]
rs2186949	0.85[EUR][1000 genomes]
rs2781233	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs589151	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs602601	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs604369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs604814	0.96[CEU][hapmap];0.91[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs6688558	1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6696891	0.85[AFR][1000 genomes]
rs670666	0.81[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap]
rs684016	0.84[TSI][hapmap]
rs7419116	1.00[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes]
rs7512495	0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs7543322	0.88[CEU][hapmap];0.98[GIH][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs7548453	0.88[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7555790	1.00[LWK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2274985	KIAA2013	cis	parietal	SCAN
rs2274985	APITD1	cis	cerebellum	SCAN
rs2274985	PLEKHG5	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10566400-10577800	Enhancers	Fetal Thymus	thymus
2	chr1:10566800-10579800	Enhancers	Liver	Liver
3	chr1:10568800-10576600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:10569000-10578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:10569600-10577800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:10569800-10575000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:10570200-10574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:10570800-10574400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:10570800-10574400	Weak transcription	Fetal Heart	heart
10	chr1:10570800-10579800	Weak transcription	Aorta	Aorta
11	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
12	chr1:10571000-10574400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:10571000-10574400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:10571000-10574800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:10571000-10574800	Weak transcription	Brain Germinal Matrix	brain
16	chr1:10571000-10576000	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:10571000-10576600	Weak transcription	Placenta	Placenta
18	chr1:10571000-10577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:10571000-10577000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr1:10571200-10574400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:10571200-10574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:10571200-10575800	Weak transcription	Pancreas	Pancrea
23	chr1:10571200-10576400	Weak transcription	Gastric	stomach
24	chr1:10571400-10574400	Weak transcription	Fetal Kidney	kidney
25	chr1:10571400-10574600	Genic enhancers	K562	blood
26	chr1:10571400-10579400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr1:10571600-10574200	Weak transcription	Fetal Lung	lung
28	chr1:10571600-10575800	Weak transcription	Stomach Mucosa	stomach
29	chr1:10571600-10576400	Enhancers	Primary hematopoietic stem cells	blood
30	chr1:10571600-10576800	Weak transcription	Small Intestine	intestine
31	chr1:10571600-10578000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:10571600-10579200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:10571800-10574000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:10571800-10574400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:10571800-10574400	Weak transcription	Left Ventricle	heart
36	chr1:10571800-10574600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:10571800-10574800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:10571800-10575600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr1:10571800-10575600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr1:10571800-10576000	Weak transcription	Adipose Nuclei	Adipose
41	chr1:10571800-10576400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:10571800-10576600	Enhancers	Primary T cells from cord blood	blood
43	chr1:10571800-10576600	Weak transcription	Right Ventricle	heart
44	chr1:10571800-10576800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:10571800-10577000	Weak transcription	Right Atrium	heart
46	chr1:10571800-10577200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:10571800-10577400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr1:10571800-10577400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:10571800-10577400	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr1:10571800-10578000	Enhancers	Primary T helper cells fromperipheralblood	blood

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