Variant report

Variant	rs11204791
Chromosome Location	chr1:151240542-151240543
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151225991..151228063-chr1:151240379..151242466,2	MCF-7	breast:
2	chr1:151234387..151237177-chr1:151238975..151242676,3	MCF-7	breast:
3	chr1:151225606..151229470-chr1:151239173..151241367,3	K562	blood:

Variant related genes	Relation type
ENSG00000159352	Chromatin interaction

Extended variants
information (count: 76 )
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	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];0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10788801	0.86[JPT][hapmap]
rs10788803	0.85[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10888408	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]
rs10888409	0.85[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	0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][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	0.81[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.91[JPT][hapmap]
rs2275900	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[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[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];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs4291501	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4520422	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];0.89[YRI][hapmap];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	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.82[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];0.82[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	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971021	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];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971025	0.85[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];0.82[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	0.88[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];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695344	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];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];0.94[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	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];0.87[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];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:8 , 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	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
6	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
8	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription 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	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11204791	PSMD4	cis	parietal	SCAN
rs11204791	SELENBP1	cis	cerebellum	SCAN
rs11204791	CTSS	cis	cerebellum	SCAN
rs11204791	MRPS21	cis	parietal	SCAN
rs11204791	PSMD4	cis	cerebellum	SCAN
rs11204791	ARNT	cis	parietal	SCAN
rs11204791	HORMAD1	cis	parietal	SCAN
rs11204791	GPR172A	trans	parietal	SCAN

Chromatin state (count:125 , 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	chr1:151234200-151241400	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:151234200-151243200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:151234200-151243200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:151234200-151244000	Strong transcription	Fetal Muscle Leg	muscle
24	chr1:151234200-151244200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:151234200-151244200	Strong transcription	Placenta	Placenta
26	chr1:151234200-151244400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:151234200-151244600	Strong transcription	Fetal Thymus	thymus
28	chr1:151234200-151245000	Strong transcription	Fetal Intestine Small	intestine
29	chr1:151234400-151240600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:151234400-151240600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr1:151234400-151240800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:151234400-151241400	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:151234400-151241400	Strong transcription	Thymus	Thymus
34	chr1:151234400-151241600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:151234400-151241800	Strong transcription	Brain Germinal Matrix	brain
36	chr1:151234400-151243000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:151234400-151243600	Strong transcription	Adipose Nuclei	Adipose
38	chr1:151234600-151240600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:151234600-151240600	Strong transcription	Primary T cells from cord blood	blood
40	chr1:151234600-151240600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:151234600-151240600	Strong transcription	Brain Anterior Caudate	brain
42	chr1:151234600-151240600	Strong transcription	Brain Substantia Nigra	brain
43	chr1:151234600-151240600	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr1:151234600-151240600	Strong transcription	Fetal Lung	lung
45	chr1:151234600-151240600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr1:151234600-151240600	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr1:151234600-151240600	Strong transcription	A549	lung
48	chr1:151234600-151240800	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:151234600-151240800	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr1:151234600-151240800	Strong transcription	Rectal Smooth Muscle	rectum

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