Variant report

Variant	rs4970948
Chromosome Location	chr1:151291243-151291244
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151290821..151293290-chr1:151295135..151297103,2	MCF-7	breast:
2	chr1:151277677..151279590-chr1:151290273..151292071,2	MCF-7	breast:
3	1:151289152-151293154..1:151411623-151426875	Hela-S3	cervix:
4	chr1:151290984..151293402-chr1:151302923..151305686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143393	Chromatin interaction
ENSG00000143442	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1056847	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10749660	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs10788801	0.86[JPT][hapmap]
rs10788803	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788804	0.96[CEU][hapmap];0.83[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs10888408	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]
rs10888409	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10888410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10888411	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204785	0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap]
rs11204791	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]
rs11204795	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12048670	0.86[ASN][1000 genomes]
rs12069445	0.80[EUR][1000 genomes]
rs1536617	0.91[JPT][hapmap]
rs16827941	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1752387	0.83[GIH][hapmap];0.85[JPT][hapmap]
rs1892196	0.86[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap]
rs2025900	0.82[JPT][hapmap]
rs2031797	0.88[GIH][hapmap];0.91[JPT][hapmap]
rs2275900	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]
rs2769268	0.82[JPT][hapmap]
rs2769273	0.82[JPT][hapmap]
rs2800946	0.82[JPT][hapmap]
rs3811405	0.86[JPT][hapmap]
rs3811406	0.85[GIH][hapmap];0.91[JPT][hapmap]
rs41302131	0.85[ASN][1000 genomes]
rs4246525	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4520422	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4522000	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4636463	0.90[JPT][hapmap]
rs4970944	0.85[CHB][hapmap];0.80[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap]
rs4970949	0.80[EUR][1000 genomes]
rs4971013	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs4971023	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs4971025	0.85[ASN][1000 genomes]
rs4971026	0.85[ASN][1000 genomes]
rs4971027	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971029	0.91[JPT][hapmap]
rs4971030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971031	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971032	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971033	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5022636	0.88[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6587559	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6587562	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[ASN][1000 genomes]
rs6677686	0.80[EUR][1000 genomes]
rs6678528	0.86[JPT][hapmap]
rs6681071	0.84[ASN][1000 genomes]
rs6681163	0.84[ASN][1000 genomes]
rs6686402	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs6695344	0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap]
rs744536	0.92[CEU][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7518924	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527032	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7531495	0.82[EUR][1000 genomes]
rs7532935	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7539584	0.90[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7544947	0.90[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs7545392	1.00[CEU][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7552906	1.00[CEU][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs943637	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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
2	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
3	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
4	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
5	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
6	nsv831581	chr1:151289151-151478605	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4970948	PSMD4	cis	cerebellum	SCAN
rs4970948	SELENBP1	cis	cerebellum	SCAN
rs4970948	LCE5A	cis	cerebellum	SCAN
rs4970948	PSMD4	cis	parietal	SCAN
rs4970948	HIST2H2AC	cis	parietal	SCAN
rs4970948	CTSS	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151257200-151297600	Strong transcription	Dnd41	blood
2	chr1:151257600-151293600	Strong transcription	Brain Germinal Matrix	brain
3	chr1:151258200-151297200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr1:151258400-151293400	Strong transcription	Fetal Brain Female	brain
5	chr1:151258400-151297800	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr1:151260000-151298000	Strong transcription	Thymus	Thymus
7	chr1:151261600-151297800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:151262000-151298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:151262600-151297600	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr1:151265800-151298000	Strong transcription	Fetal Thymus	thymus
11	chr1:151271400-151298800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:151273200-151298000	Strong transcription	Primary T cells from cord blood	blood
13	chr1:151273800-151297800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:151274400-151295000	Strong transcription	Primary B cells from cord blood	blood
15	chr1:151280200-151299200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:151280400-151299000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:151283200-151298000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:151283200-151299000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr1:151283400-151296000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:151283400-151297400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:151284600-151292400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:151284800-151292800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:151284800-151295200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:151285000-151297200	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:151285200-151291600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:151285200-151295400	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:151285200-151297400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr1:151285400-151294400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:151285600-151292200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr1:151285600-151298000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:151285800-151294400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr1:151286000-151294600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:151286400-151297800	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr1:151286800-151298400	Strong transcription	Fetal Intestine Large	intestine
35	chr1:151287000-151291800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:151287000-151292400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:151287000-151298400	Weak transcription	Small Intestine	intestine
38	chr1:151287000-151298600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr1:151287200-151291800	Strong transcription	Fetal Intestine Small	intestine
40	chr1:151287200-151292600	Strong transcription	Spleen	Spleen
41	chr1:151287200-151293000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:151287200-151294600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:151287200-151295400	Strong transcription	Fetal Lung	lung
44	chr1:151287200-151296200	Weak transcription	Stomach Mucosa	stomach
45	chr1:151287200-151297800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:151287200-151298000	Weak transcription	Fetal Heart	heart
47	chr1:151287400-151292000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:151287400-151293000	Weak transcription	Psoas Muscle	Psoas
49	chr1:151287400-151293600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:151287400-151297000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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