Variant report

Variant	rs2274739
Chromosome Location	chr1:153612133-153612134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153548195..153551258-chr1:153612052..153615692,3	MCF-7	breast:
2	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
3	chr1:153610724..153613388-chr1:153700674..153702606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196754	Chromatin interaction
ENSG00000143624	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1046381	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10797056	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];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797090	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10797096	0.88[JPT][hapmap]
rs10908746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908848	0.88[JPT][hapmap]
rs11265625	0.88[JPT][hapmap]
rs11265633	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1128894	0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11497739	0.82[TSI][hapmap]
rs11548103	0.82[EUR][1000 genomes]
rs11548104	0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs11580122	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139953	0.85[ASN][1000 genomes]
rs12564925	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730186	0.88[ASN][1000 genomes]
rs1411273	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1810836	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1888115	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274740	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];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28380060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28416529	0.85[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs28510471	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28518786	0.93[ASN][1000 genomes]
rs28580554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28613361	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28700217	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28754733	0.83[CHD][hapmap]
rs3790411	0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3790412	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3795396	0.92[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806233	0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs3806234	0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs3818632	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828031	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862047	0.86[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs4351684	0.92[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4515830	0.89[JPT][hapmap]
rs4845557	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845558	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4845560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845563	0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6427640	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66721814	0.85[ASN][1000 genomes]
rs6674929	0.88[JPT][hapmap]
rs6694006	0.82[AMR][1000 genomes]
rs7345	0.92[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7541193	0.80[MEX][hapmap]
rs7934	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs913860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913861	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9330298	0.84[CHB][hapmap]
rs9330299	0.80[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs9330300	0.82[EUR][1000 genomes]
rs9330301	0.80[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs9661993	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9662664	0.88[JPT][hapmap]
rs9729773	0.82[EUR][1000 genomes]
rs985242	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs999418	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs2274739	S100A4	cis	lymphoblastoid	seeQTL
rs2274739	S100A16	cis	parietal	SCAN
rs2274739	S100A13	cis	multi-tissue	Pritchard
rs2274739	FLG	cis	cerebellum	SCAN
rs2274739	S100A13	cis	Adipose Subcutaneous	GTEx
rs2274739	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs2274739	S100A13	cis	parietal	SCAN
rs2274739	SLC27A3	cis	cerebellum	SCAN
rs2274739	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs2274739	RP1-178F15.4	cis	Skin Sun Exposed Lower leg	GTEx
rs2274739	CHTOP	cis	Muscle Skeletal	GTEx
rs2274739	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs2274739	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs2274739	S100A2	cis	cerebellum	SCAN
rs2274739	S100A13	cis	lymphoblastoid	seeQTL
rs2274739	S100A16	cis	cerebellum	SCAN
rs2274739	S100A10	cis	cerebellum	SCAN
rs2274739	RP1-178F15.4	cis	Artery Aorta	GTEx
rs2274739	RP1-178F15.4	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153608200-153613200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:153608200-153618600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:153608200-153618800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr1:153608200-153619600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:153608400-153616400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:153608400-153618600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:153608400-153618800	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr1:153608400-153618800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:153608400-153619200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr1:153608400-153619200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:153608400-153619800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:153608600-153615600	Strong transcription	Fetal Intestine Large	intestine
13	chr1:153608600-153618600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr1:153608600-153618800	Strong transcription	HUVEC	blood vessel
15	chr1:153608600-153619400	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:153608600-153619400	Strong transcription	Osteobl	bone
17	chr1:153608600-153619600	Strong transcription	Primary hematopoietic stem cells	blood
18	chr1:153608600-153619600	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:153608600-153619600	Strong transcription	HMEC	breast
20	chr1:153608600-153620200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:153608600-153620200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:153608800-153612200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr1:153608800-153618400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:153608800-153618800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:153608800-153619400	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:153608800-153619800	Strong transcription	Rectal Mucosa Donor 31	rectum
27	chr1:153608800-153620200	Strong transcription	Fetal Thymus	thymus
28	chr1:153609000-153613000	Strong transcription	Fetal Kidney	kidney
29	chr1:153609000-153616200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:153609000-153616600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:153609000-153617000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
32	chr1:153609000-153618600	Strong transcription	Placenta Amnion	Placenta Amnion
33	chr1:153609200-153612200	Genic enhancers	Fetal Heart	heart
34	chr1:153609200-153613000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:153609200-153614600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr1:153609200-153617600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr1:153609200-153618800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:153609200-153619400	Strong transcription	Spleen	Spleen
39	chr1:153609200-153620000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:153609200-153620000	Strong transcription	Fetal Brain Female	brain
41	chr1:153609200-153620200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:153609400-153612200	Strong transcription	Colonic Mucosa	Colon
43	chr1:153609400-153618800	Strong transcription	Fetal Lung	lung
44	chr1:153609400-153618800	Strong transcription	NH-A	brain
45	chr1:153609400-153619000	Strong transcription	Thymus	Thymus
46	chr1:153609600-153612600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr1:153609600-153613200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:153609600-153613200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:153609600-153613400	Strong transcription	Colon Smooth Muscle	Colon
50	chr1:153609600-153614400	Strong transcription	GM12878-XiMat	blood

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