Variant report

Variant	rs11204785
Chromosome Location	chr1:151150857-151150858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151002944..151005069-chr1:151149022..151151363,2	MCF-7	breast:
2	chr1:151137725..151143993-chr1:151144904..151151967,18	K562	blood:
3	chr1:151147180..151151121-chr1:151169846..151172495,3	MCF-7	breast:
4	chr1:151146491..151149385-chr1:151149619..151151177,2	MCF-7	breast:
5	chr1:151042978..151045124-chr1:151149894..151152282,2	MCF-7	breast:
6	chr1:151149446..151154137-chr1:151160339..151164004,6	K562	blood:

Variant related genes	Relation type
ENSG00000163156	Chromatin interaction
ENSG00000163157	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000163159	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1056847	0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10749660	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10788801	0.90[JPT][hapmap]
rs10788803	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs10888406	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888408	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]
rs10888409	0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs10888410	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs11204791	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]
rs11807075	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12022732	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12062719	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12080778	0.83[EUR][1000 genomes]
rs12407426	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1536617	0.85[JPT][hapmap]
rs16827941	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16833079	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1752387	0.81[JPT][hapmap]
rs1892196	0.90[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2025900	0.86[JPT][hapmap]
rs2031797	0.85[JPT][hapmap]
rs2275900	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]
rs2769268	0.86[JPT][hapmap]
rs2769273	0.86[JPT][hapmap]
rs2800946	0.86[JPT][hapmap]
rs3811405	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs3811406	0.85[JPT][hapmap]
rs41302131	0.80[EUR][1000 genomes]
rs4246525	0.85[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4291501	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4520422	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4636463	0.90[GIH][hapmap];0.85[JPT][hapmap]
rs4970943	0.81[AMR][1000 genomes]
rs4970944	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4970948	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs4971013	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971015	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971016	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971018	0.85[JPT][hapmap]
rs4971021	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971023	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971025	0.82[EUR][1000 genomes]
rs4971026	0.83[EUR][1000 genomes]
rs4971027	0.85[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs4971029	0.85[JPT][hapmap]
rs4971030	0.85[CHB][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap]
rs5022636	0.86[JPT][hapmap]
rs58323986	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61817972	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6587559	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6587562	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs6678528	0.90[JPT][hapmap]
rs6681071	0.83[EUR][1000 genomes]
rs6681163	0.83[EUR][1000 genomes]
rs6683396	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6686402	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6695344	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs6701325	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7521064	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7527032	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7532935	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7539584	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7544947	0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7545392	0.90[JPT][hapmap]
rs7552906	0.86[JPT][hapmap]
rs943637	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]

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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs11204785	SELENBP1	cis	cerebellum	SCAN
rs11204785	CTSK	cis	cerebellum	SCAN
rs11204785	ANKRD34A	cis	cerebellum	SCAN
rs11204785	VPS45	cis	cerebellum	SCAN
rs11204785	MRPS21	cis	parietal	SCAN
rs11204785	CTSS	cis	cerebellum	SCAN
rs11204785	ARNT	cis	parietal	SCAN
rs11204785	PSMD4	cis	cerebellum	SCAN
rs11204785	PSMD4	cis	parietal	SCAN
rs11204785	MLLT11	cis	parietal	SCAN
rs11204785	FLG	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151139600-151158600	Strong transcription	Fetal Stomach	stomach
2	chr1:151139600-151158600	Strong transcription	Lung	lung
3	chr1:151139600-151161600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:151139800-151158600	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr1:151139800-151158600	Strong transcription	Fetal Intestine Small	intestine
6	chr1:151139800-151159000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:151139800-151159400	Strong transcription	Fetal Brain Female	brain
8	chr1:151140000-151153400	Strong transcription	Placenta	Placenta
9	chr1:151140000-151158600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:151140000-151158600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:151140000-151158600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:151140000-151158600	Strong transcription	Fetal Intestine Large	intestine
13	chr1:151140000-151158600	Strong transcription	Fetal Thymus	thymus
14	chr1:151140000-151158600	Strong transcription	Spleen	Spleen
15	chr1:151140000-151158800	Strong transcription	Primary B cells from peripheral blood	blood
16	chr1:151140000-151158800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:151140000-151159200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:151140000-151159200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:151140000-151160000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:151140000-151160800	Weak transcription	Stomach Mucosa	stomach
21	chr1:151140600-151158600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:151140600-151158600	Strong transcription	Thymus	Thymus
23	chr1:151140600-151159800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:151140800-151159000	Strong transcription	Primary T cells fromperipheralblood	blood
25	chr1:151144000-151153600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:151144000-151155000	Weak transcription	NHDF-Ad	bronchial
27	chr1:151145600-151158400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:151145600-151158600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:151145600-151158800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:151145800-151151400	Strong transcription	Primary B cells from cord blood	blood
31	chr1:151145800-151151600	Strong transcription	GM12878-XiMat	blood
32	chr1:151145800-151157000	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr1:151145800-151158400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr1:151145800-151158600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr1:151145800-151158600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr1:151145800-151158800	Strong transcription	Primary T cells from cord blood	blood
37	chr1:151145800-151158800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:151145800-151158800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:151145800-151159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:151145800-151159600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:151145800-151160200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:151146000-151158600	Strong transcription	Liver	Liver
43	chr1:151146000-151158800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:151146000-151158800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:151146000-151159000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:151146400-151158600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:151146400-151160400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:151146400-151160800	Weak transcription	Fetal Heart	heart
49	chr1:151146600-151151600	Strong transcription	NHEK	skin
50	chr1:151146600-151158400	Strong transcription	Rectal Mucosa Donor 31	rectum

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