Variant report

Variant	rs7554916
Chromosome Location	chr1:113123734-113123735
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113120348..113122221-chr1:113122499..113124584,2	K562	blood:
2	chr1:113120564..113122444-chr1:113122780..113125014,2	MCF-7	breast:
3	chr1:113122500..113125301-chr1:113129408..113131758,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1001494	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1006298	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10745330	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10776755	0.85[CEU][hapmap];0.81[GIH][hapmap];0.87[TSI][hapmap]
rs10776756	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10776757	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10857963	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102497	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102512	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584092	0.85[CEU][hapmap]
rs12046208	0.85[CEU][hapmap];0.83[GIH][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap]
rs12046329	0.85[AMR][1000 genomes]
rs12046466	0.86[AMR][1000 genomes]
rs12126277	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728001	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994604	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932532	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs2932536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2999154	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs2999155	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes]
rs2999157	0.83[AMR][1000 genomes]
rs3013439	0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3013440	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3103450	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs351372	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4838959	0.81[GIH][hapmap];0.91[TSI][hapmap]
rs4839254	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6537743	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537748	0.81[GIH][hapmap];0.83[TSI][hapmap]
rs6537749	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs6666579	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][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]
rs6669096	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679414	0.82[EUR][1000 genomes]
rs6682737	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691932	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6700673	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7415820	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.99[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7513716	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7524494	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7544663	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7546094	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7554345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs902289	0.96[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes]
rs910697	0.92[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9429486	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs7554916	CAPZA1	Cis_1M	lymphoblastoid	RTeQTL
rs7554916	ST7L	cis	normal skin	skin_eQTL
rs7554916	ST7L	cis	Thyroid	GTEx
rs7554916	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs7554916	ST7L	cis	Heart Left Ventricle	GTEx
rs7554916	ST7L	cis	Nerve Tibial	GTEx
rs7554916	ST7L	cis	Adipose Subcutaneous	GTEx
rs7554916	ST7L	cis	lung	GTEx
rs7554916	ST7L	cis	Lymphoblastoid	GTEx
rs7554916	ST7L	cis	lesional skin	skin_eQTL
rs7554916	ST7L	cis	multi-tissue	Pritchard
rs7554916	ST7L	cis	Artery Tibial	GTEx
rs7554916	ST7L	cis	uninvolved skin	skin_eQTL
rs7554916	ST7L	cis	lymphoblastoid	seeQTL
rs7554916	ST7L	cis	Stomach	GTEx
rs7554916	ST7L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
2	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
5	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
6	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:113087600-113125800	Weak transcription	Colon Smooth Muscle	Colon
11	chr1:113088400-113132200	Weak transcription	HMEC	breast
12	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
13	chr1:113105400-113129800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:113109000-113160000	Weak transcription	Gastric	stomach
15	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:113111000-113131000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:113111800-113138800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:113112000-113128200	Strong transcription	Liver	Liver
19	chr1:113112600-113131800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:113113200-113124400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:113113200-113132400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:113113800-113124400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr1:113114400-113124600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:113115000-113128800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:113115200-113123800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:113115200-113130200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:113115400-113123800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
29	chr1:113115800-113130800	Weak transcription	Fetal Brain Male	brain
30	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
31	chr1:113116000-113132400	Weak transcription	Thymus	Thymus
32	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
33	chr1:113116800-113124800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:113117000-113132200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:113117200-113125600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:113117200-113132200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:113117200-113132400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr1:113117400-113124000	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:113117400-113125000	Strong transcription	Adipose Nuclei	Adipose
40	chr1:113117400-113132200	Weak transcription	GM12878-XiMat	blood
41	chr1:113117800-113124600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:113118400-113132400	Weak transcription	Brain Substantia Nigra	brain
44	chr1:113118600-113123800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:113118600-113132200	Weak transcription	A549	lung
46	chr1:113118800-113124800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:113118800-113126800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:113118800-113131200	Weak transcription	Brain Angular Gyrus	brain
49	chr1:113118800-113132200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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