Variant report

Variant	rs1535922
Chromosome Location	chr13:49762956-49762957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:49762820-49763108	K562	blood:	n/a	n/a

Variant related genes	Relation type
COX7CP1	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1013347	0.84[AMR][1000 genomes]
rs12184794	0.81[AMR][1000 genomes]
rs12871418	0.82[AMR][1000 genomes]
rs1359066	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1407827	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs1407829	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1928109	0.86[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs1937180	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1937181	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes]
rs1983805	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2026029	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs2075610	0.89[GIH][hapmap]
rs2146748	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2147399	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2149498	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2181539	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs2183095	0.83[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2407266	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2897633	1.00[CEU][hapmap];0.81[CHB][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2897689	0.85[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2987528	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs2994377	1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994378	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2994379	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs2994380	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3012116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3012117	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs3012121	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs3012127	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap]
rs3012136	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs34360275	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35018425	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4142065	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4245350	0.96[EUR][1000 genomes]
rs4530025	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4942796	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4942799	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4942800	0.95[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs6561496	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs6561497	0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.83[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap]
rs6561504	0.95[CEU][hapmap];0.82[CHB][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6561506	0.81[AMR][1000 genomes]
rs6561507	0.81[AMR][1000 genomes]
rs67235936	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7139746	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7139819	0.92[EUR][1000 genomes]
rs716722	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs728075	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs7317908	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7329291	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs7331917	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7333097	0.82[CHB][hapmap]
rs7333285	0.95[CEU][hapmap];0.82[CHB][hapmap];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7338304	0.81[AMR][1000 genomes]
rs7338529	0.95[CEU][hapmap];0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs736222	0.82[JPT][hapmap]
rs7983885	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7986624	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs7987258	0.87[CEU][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap]
rs7988168	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs7989175	0.82[CHB][hapmap]
rs7990573	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7994845	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7994910	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7995616	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs7996151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316426	0.95[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs9316428	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9316429	0.82[CHB][hapmap]
rs9526518	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9526521	1.00[GIH][hapmap]
rs9526525	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9526526	0.80[EUR][1000 genomes]
rs9526531	0.82[AMR][1000 genomes]
rs9526532	0.82[GIH][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes]
rs9535126	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs9535136	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9535145	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535146	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9535147	0.95[CEU][hapmap];0.82[CHB][hapmap]
rs9535149	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs9535154	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535155	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535156	0.95[CEU][hapmap];0.82[CHB][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535166	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[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];0.96[ASN][1000 genomes]
rs9535167	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535170	0.82[AMR][1000 genomes]
rs9535172	0.85[AMR][1000 genomes]
rs9562866	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap]
rs9562870	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568150	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs9568151	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs9568169	0.89[GIH][hapmap];0.85[MKK][hapmap];0.82[AMR][1000 genomes]
rs9568171	0.81[AMR][1000 genomes]
rs9568172	0.82[AMR][1000 genomes]
rs9568173	0.81[AMR][1000 genomes]
rs9596064	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596073	0.81[AMR][1000 genomes]
rs972297	1.00[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1535922	SERP2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49687600-49789000	Weak transcription	Stomach Mucosa	stomach
2	chr13:49724400-49765000	Weak transcription	A549	lung
3	chr13:49737800-49788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:49738000-49777000	Weak transcription	Small Intestine	intestine
5	chr13:49738400-49785200	Strong transcription	Liver	Liver
6	chr13:49738600-49785000	Strong transcription	Dnd41	blood
7	chr13:49739000-49768200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr13:49739000-49774200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:49739600-49786400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:49740200-49786000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:49740400-49784800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr13:49740600-49768400	Strong transcription	Fetal Thymus	thymus
13	chr13:49740600-49769000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr13:49740600-49772800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr13:49740600-49786600	Strong transcription	Placenta	Placenta
16	chr13:49741600-49783400	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr13:49742600-49783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:49742800-49774400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:49745600-49783400	Strong transcription	Duodenum Mucosa	Duodenum
20	chr13:49747400-49764000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr13:49747400-49766400	Weak transcription	Aorta	Aorta
22	chr13:49747400-49772000	Weak transcription	Esophagus	oesophagus
23	chr13:49747400-49772000	Weak transcription	Spleen	Spleen
24	chr13:49748800-49790600	Weak transcription	K562	blood
25	chr13:49749400-49767600	Strong transcription	Primary hematopoietic stem cells	blood
26	chr13:49749400-49768200	Strong transcription	Fetal Intestine Large	intestine
27	chr13:49749400-49774000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr13:49750200-49769000	Strong transcription	Fetal Muscle Leg	muscle
29	chr13:49750800-49766200	Strong transcription	HSMM	muscle
30	chr13:49750800-49768400	Strong transcription	Fetal Muscle Trunk	muscle
31	chr13:49751200-49768200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr13:49751400-49767800	Strong transcription	NH-A	brain
33	chr13:49752600-49763200	Strong transcription	HSMMtube	muscle
34	chr13:49753200-49766400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:49753200-49766400	Weak transcription	Lung	lung
36	chr13:49753200-49767400	Weak transcription	Gastric	stomach
37	chr13:49753200-49787600	Weak transcription	Psoas Muscle	Psoas
38	chr13:49753400-49765200	Weak transcription	Brain Angular Gyrus	brain
39	chr13:49753400-49772000	Weak transcription	Colonic Mucosa	Colon
40	chr13:49754800-49769400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr13:49756600-49785400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:49756600-49786400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:49756800-49763000	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr13:49756800-49782800	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr13:49757000-49763000	Strong transcription	Primary B cells from cord blood	blood
46	chr13:49757000-49768800	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr13:49757000-49769600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:49757200-49767000	Strong transcription	Primary T cells from cord blood	blood
49	chr13:49757200-49774400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr13:49757600-49771800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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