Variant report

Variant	rs10888408
Chromosome Location	chr1:151239570-151239571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151234387..151237177-chr1:151238975..151242676,3	MCF-7	breast:
2	chr1:151236628..151240261-chr1:151252418..151256646,5	K562	blood:
3	chr1:151234077..151236106-chr1:151238439..151240160,2	MCF-7	breast:
4	chr1:151225606..151229470-chr1:151239173..151241367,3	K562	blood:

Variant related genes	Relation type
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000159352	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1056847	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10749660	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788801	0.86[JPT][hapmap]
rs10788803	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10888409	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10888410	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11204785	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs11204791	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204795	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12022732	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040384	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12048670	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12062719	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12080778	0.89[EUR][1000 genomes]
rs12407426	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1536617	0.91[JPT][hapmap]
rs16827941	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833079	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1752387	0.85[JPT][hapmap]
rs1892196	0.94[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.91[JPT][hapmap]
rs2275900	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2769268	0.82[JPT][hapmap]
rs2769273	0.82[JPT][hapmap]
rs2800946	0.82[JPT][hapmap]
rs3811405	0.86[GIH][hapmap];0.86[JPT][hapmap]
rs3811406	0.91[JPT][hapmap]
rs41302131	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4246525	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.84[ASN][1000 genomes]
rs4291501	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4520422	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4522000	0.88[ASN][1000 genomes]
rs4636463	0.90[GIH][hapmap];0.90[JPT][hapmap]
rs4970944	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4970948	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs4971013	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971015	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4971016	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971021	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971023	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971025	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971026	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971027	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4971029	0.91[JPT][hapmap]
rs4971030	0.90[CHB][hapmap];0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4971032	0.85[ASN][1000 genomes]
rs5022636	0.81[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap]
rs58323986	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61817972	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6587559	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587562	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6681071	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681163	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683396	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6686402	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695344	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6701325	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7518924	0.85[ASN][1000 genomes]
rs7521064	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527032	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532935	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539584	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544947	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545392	0.95[JPT][hapmap]
rs7552906	0.91[JPT][hapmap]
rs943637	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10888408	MRPS21	cis	parietal	SCAN
rs10888408	SELENBP1	cis	cerebellum	SCAN
rs10888408	PSMD4	cis	parietal	SCAN
rs10888408	GPR172A	trans	parietal	SCAN
rs10888408	ARNT	cis	parietal	SCAN
rs10888408	PSMD4	cis	cerebellum	SCAN
rs10888408	CTSS	cis	cerebellum	SCAN
rs10888408	HORMAD1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151228400-151244000	Weak transcription	Right Atrium	heart
2	chr1:151228400-151253400	Weak transcription	Fetal Brain Male	brain
3	chr1:151228600-151244400	Weak transcription	Fetal Heart	heart
4	chr1:151230600-151244400	Strong transcription	Fetal Stomach	stomach
5	chr1:151231200-151243200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:151231800-151243400	Strong transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:151232800-151244400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:151232800-151244400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:151233800-151242800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:151233800-151243200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:151233800-151244400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:151234000-151240600	Strong transcription	Dnd41	blood
13	chr1:151234000-151240600	Strong transcription	HMEC	breast
14	chr1:151234000-151240800	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:151234000-151240800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:151234000-151241800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:151234000-151243200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:151234000-151244400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:151234000-151245000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:151234200-151240000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:151234200-151240200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:151234200-151241400	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:151234200-151243200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:151234200-151243200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:151234200-151244000	Strong transcription	Fetal Muscle Leg	muscle
26	chr1:151234200-151244200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:151234200-151244200	Strong transcription	Placenta	Placenta
28	chr1:151234200-151244400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr1:151234200-151244600	Strong transcription	Fetal Thymus	thymus
30	chr1:151234200-151245000	Strong transcription	Fetal Intestine Small	intestine
31	chr1:151234400-151240600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:151234400-151240600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:151234400-151240800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:151234400-151241400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:151234400-151241400	Strong transcription	Thymus	Thymus
36	chr1:151234400-151241600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:151234400-151241800	Strong transcription	Brain Germinal Matrix	brain
38	chr1:151234400-151243000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:151234400-151243600	Strong transcription	Adipose Nuclei	Adipose
40	chr1:151234600-151239600	Strong transcription	NHEK	skin
41	chr1:151234600-151239800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:151234600-151239800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:151234600-151240000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:151234600-151240200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
45	chr1:151234600-151240400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:151234600-151240400	Strong transcription	Hela-S3	cervix
47	chr1:151234600-151240600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr1:151234600-151240600	Strong transcription	Primary T cells from cord blood	blood
49	chr1:151234600-151240600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:151234600-151240600	Strong transcription	Brain Anterior Caudate	brain

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