Variant report

Variant	rs10797096
Chromosome Location	chr1:153640665-153640666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153604920..153606894-chr1:153640638..153643940,3	K562	blood:
2	chr1:153638812..153642214-chr1:153649454..153652124,3	MCF-7	breast:
3	chr1:153638167..153640842-chr1:153716743..153718282,2	K562	blood:
4	chr1:153598025..153599880-chr1:153638172..153641128,3	K562	blood:
5	chr1:153581285..153583404-chr1:153640253..153643290,3	MCF-7	breast:
6	chr1:153638977..153641528-chr1:153700194..153703365,4	K562	blood:

Variant related genes	Relation type
ENSG00000271853	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000188643	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10797056	0.88[JPT][hapmap]
rs10797090	0.80[ASN][1000 genomes]
rs10908848	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265625	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265633	0.93[ASN][1000 genomes]
rs11548102	0.84[EUR][1000 genomes]
rs11588347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12139953	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12564925	0.88[JPT][hapmap]
rs12730186	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12755890	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1888115	0.88[JPT][hapmap]
rs2274739	0.88[JPT][hapmap]
rs2274740	0.88[JPT][hapmap]
rs28380060	0.88[JPT][hapmap]
rs28518786	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28580554	0.88[JPT][hapmap]
rs28754733	0.88[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3790411	0.82[JPT][hapmap]
rs3790412	0.88[JPT][hapmap]
rs3795396	0.95[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs3806233	0.88[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs3806234	0.92[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3818632	0.88[JPT][hapmap]
rs3828031	0.88[JPT][hapmap]
rs3862047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[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];0.95[ASN][1000 genomes]
rs4072425	0.85[CEU][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs4310476	0.82[AMR][1000 genomes]
rs4351684	0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4515830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs4845563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845564	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55772653	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427640	0.87[ASN][1000 genomes]
rs66721814	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6674929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7345	0.95[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7934	0.88[JPT][hapmap]
rs913860	0.80[CHB][hapmap]
rs913861	0.88[JPT][hapmap]
rs9330298	0.84[CEU][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs9661993	0.90[ASN][1000 genomes]
rs9662664	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9700179	0.80[CEU][hapmap];0.82[TSI][hapmap]
rs9700928	0.81[CEU][hapmap];0.82[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs9726753	0.85[EUR][1000 genomes]
rs9792963	0.84[EUR][1000 genomes]
rs9792967	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs10797096	S100A2	cis	cerebellum	SCAN
rs10797096	S100A13	cis	Adipose Subcutaneous	GTEx
rs10797096	S100A16	cis	cerebellum	SCAN
rs10797096	SCNM1	cis	parietal	SCAN
rs10797096	S100A13	cis	parietal	SCAN
rs10797096	SLC27A3	cis	cerebellum	SCAN
rs10797096	RP1-178F15.4	cis	Adipose Subcutaneous	GTEx
rs10797096	S100A13	cis	lymphoblastoid	seeQTL
rs10797096	RP1-178F15.5	cis	Adipose Subcutaneous	GTEx
rs10797096	S100A13	Cis_1M	lymphoblastoid	RTeQTL
rs10797096	S100A10	cis	cerebellum	SCAN
rs10797096	DCST2	cis	parietal	SCAN
rs10797096	S100A9	cis	parietal	SCAN
rs10797096	S100A4	cis	lymphoblastoid	seeQTL
rs10797096	S100A16	cis	parietal	SCAN
rs10797096	RP1-178F15.4	cis	Muscle Skeletal	GTEx
rs10797096	S100A13	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153632000-153642200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:153632000-153642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:153632400-153640800	Strong transcription	Fetal Muscle Leg	muscle
4	chr1:153632400-153641200	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:153632400-153641600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:153632400-153641800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:153632400-153642000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153632400-153642400	Weak transcription	Right Atrium	heart
9	chr1:153632600-153640800	Strong transcription	Brain Germinal Matrix	brain
10	chr1:153632600-153641200	Strong transcription	Placenta	Placenta
11	chr1:153632600-153641200	Strong transcription	Fetal Thymus	thymus
12	chr1:153632600-153641400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:153632600-153641400	Strong transcription	Brain Cingulate Gyrus	brain
14	chr1:153632600-153641600	Strong transcription	Lung	lung
15	chr1:153632600-153641800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:153632600-153641800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:153632600-153641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:153632600-153641800	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:153632600-153641800	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:153632600-153642200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:153632600-153642200	Strong transcription	Fetal Stomach	stomach
22	chr1:153632800-153641800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:153632800-153641800	Strong transcription	Fetal Intestine Large	intestine
24	chr1:153632800-153642000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:153632800-153642000	Strong transcription	Fetal Intestine Small	intestine
26	chr1:153633000-153642000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr1:153633000-153642000	Strong transcription	Primary B cells from peripheral blood	blood
28	chr1:153633200-153640800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:153633200-153640800	Strong transcription	Primary B cells from cord blood	blood
30	chr1:153633200-153640800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr1:153633200-153640800	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:153633200-153640800	Strong transcription	Thymus	Thymus
33	chr1:153633200-153641000	Strong transcription	Rectal Smooth Muscle	rectum
34	chr1:153633200-153641200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr1:153633200-153641200	Strong transcription	Fetal Brain Female	brain
36	chr1:153633200-153641400	Strong transcription	Left Ventricle	heart
37	chr1:153633200-153641600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr1:153633200-153641600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:153633200-153641600	Strong transcription	Right Ventricle	heart
40	chr1:153633200-153641800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:153633200-153641800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:153633200-153641800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:153633200-153641800	Strong transcription	Colon Smooth Muscle	Colon
44	chr1:153633200-153641800	Strong transcription	HSMM	muscle
45	chr1:153633200-153642000	Strong transcription	Brain Hippocampus Middle	brain
46	chr1:153633200-153642000	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:153633400-153640800	Strong transcription	GM12878-XiMat	blood
48	chr1:153633400-153641000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:153633400-153641000	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:153633400-153641600	Strong transcription	HUES6 Cell Line	embryonic stem cell

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