Variant report

Variant	rs1778335
Chromosome Location	chr10:22932148-22932149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:22894884..22897373-chr10:22931733..22933332,2	K562	blood:
2	chr10:22902985..22904856-chr10:22930809..22933624,2	MCF-7	breast:
3	chr10:22916861..22924296-chr10:22924379..22934526,17	K562	blood:
4	chr10:22930057..22932318-chr10:22937347..22939667,3	K562	blood:
5	chr10:22922677..22924521-chr10:22929948..22932446,2	MCF-7	breast:

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10764339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10764344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10828323	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10828324	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10828325	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10828328	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs11013052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11013059	0.83[ASN][1000 genomes]
rs11013066	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11013067	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11013068	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11013077	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11013082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11013091	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1171489	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1171490	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1171492	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1171493	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1171494	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1171497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1171499	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1171503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes]
rs1171504	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1171506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs1171509	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.94[TSI][hapmap]
rs12246676	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12253847	1.00[CHB][hapmap]
rs12354766	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12356117	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12357289	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs12357384	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12357444	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12358560	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12770214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12774725	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1326340	0.82[EUR][1000 genomes]
rs1326342	0.95[YRI][hapmap]
rs1343504	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1409393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409394	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1409395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1539628	0.88[GIH][hapmap];0.81[TSI][hapmap]
rs1614387	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1620658	0.90[YRI][hapmap]
rs1750747	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs1750748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1750767	0.86[YRI][hapmap]
rs1750773	0.90[YRI][hapmap]
rs1750775	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1750777	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1750778	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778324	0.95[YRI][hapmap]
rs1778325	0.95[YRI][hapmap]
rs1778326	0.90[YRI][hapmap]
rs1778329	0.95[YRI][hapmap]
rs1778330	0.90[YRI][hapmap]
rs1778332	0.94[YRI][hapmap]
rs1778334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1778339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778340	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778342	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1778345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1778346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2031620	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2154053	0.92[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs2559534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2798981	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34208652	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34786070	0.86[ASN][1000 genomes]
rs35885150	0.83[ASN][1000 genomes]
rs7071306	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7912132	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7921549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs943196	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs943197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs943198	0.86[ASN][1000 genomes]
rs9645524	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1830947	chr10:22881196-23004381	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv831809	chr10:22918101-23069676	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1778335	PIP4K2A	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22915000-22951800	Weak transcription	Fetal Intestine Small	intestine
2	chr10:22915200-22935600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:22915200-22936200	Weak transcription	Psoas Muscle	Psoas
4	chr10:22915400-22935400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:22919800-22935000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr10:22920000-22935000	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr10:22920000-22936400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:22920200-22935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr10:22920800-22933600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr10:22921000-22933000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:22921000-22940400	Weak transcription	Ovary	ovary
12	chr10:22921200-22935000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr10:22921200-22935400	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr10:22922800-22933000	Weak transcription	Lung	lung
15	chr10:22923000-22937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:22923200-22932400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:22923200-22936200	Weak transcription	Esophagus	oesophagus
18	chr10:22926000-22938600	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr10:22926200-22935200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr10:22926800-22932200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:22926800-22932400	Weak transcription	Fetal Thymus	thymus
22	chr10:22926800-22932400	Weak transcription	Pancreas	Pancrea
23	chr10:22926800-22932600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr10:22926800-22933000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr10:22926800-22933000	Weak transcription	Spleen	Spleen
26	chr10:22926800-22935000	Weak transcription	Thymus	Thymus
27	chr10:22926800-22936200	Weak transcription	HSMMtube	muscle
28	chr10:22927000-22936200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr10:22927000-22936200	Weak transcription	Right Ventricle	heart
30	chr10:22927800-22942800	Enhancers	Brain Anterior Caudate	brain
31	chr10:22928200-22932600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr10:22929200-22938600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr10:22929400-22934200	Enhancers	Brain Substantia Nigra	brain
34	chr10:22929600-22932400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr10:22929600-22932800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr10:22929600-22935600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr10:22929600-22948400	Enhancers	Brain Cingulate Gyrus	brain
38	chr10:22929800-22932400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:22929800-22939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr10:22930200-22932800	Weak transcription	GM12878-XiMat	blood
41	chr10:22930400-22935400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:22930400-22938600	Enhancers	Brain Hippocampus Middle	brain
43	chr10:22930600-22934600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr10:22930800-22935000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr10:22930800-22935000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr10:22931000-22932600	Weak transcription	Aorta	Aorta
47	chr10:22931000-22933000	Strong transcription	Primary B cells from cord blood	blood
48	chr10:22931000-22934800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr10:22931000-22935000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr10:22931000-22935200	Enhancers	Primary T helper cells fromperipheralblood	blood

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