Variant report

Variant	rs2897689
Chromosome Location	chr13:49774553-49774554
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1359066	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs1407827	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap]
rs1407829	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs1535922	0.85[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs1937181	0.85[CEU][hapmap]
rs1983805	0.90[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs2026029	0.90[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs2075610	0.80[GIH][hapmap]
rs2146748	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs2181539	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs2407266	0.85[CEU][hapmap]
rs2897633	0.85[CEU][hapmap];0.90[CHD][hapmap];0.82[TSI][hapmap]
rs2987528	0.85[CEU][hapmap]
rs2994377	0.85[CEU][hapmap]
rs2994378	0.85[CEU][hapmap]
rs2994379	0.85[CEU][hapmap]
rs2994380	0.85[CEU][hapmap]
rs3012116	0.85[CEU][hapmap]
rs3012117	0.85[CEU][hapmap]
rs3012121	0.85[CEU][hapmap]
rs3012127	0.85[CEU][hapmap]
rs35018425	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4142065	0.80[CEU][hapmap];0.93[CHD][hapmap]
rs4245350	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4530025	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs4942796	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];0.90[YRI][hapmap]
rs4942799	0.90[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.87[MKK][hapmap];0.86[YRI][hapmap]
rs4942800	0.90[CEU][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap]
rs6561496	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs6561497	0.93[CHD][hapmap]
rs6561504	0.90[CEU][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67235936	0.82[EUR][1000 genomes]
rs7139746	0.81[EUR][1000 genomes]
rs7139819	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs716722	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7317908	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7333097	0.92[ASW][hapmap];0.95[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs7333285	0.90[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7338529	0.90[CEU][hapmap]
rs7983885	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs7987258	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.92[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap]
rs7988168	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs7989175	0.92[ASW][hapmap];0.93[CHD][hapmap];0.90[LWK][hapmap];1.00[YRI][hapmap]
rs7994845	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7994910	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.92[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap]
rs7995616	0.90[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.85[MKK][hapmap];0.86[YRI][hapmap]
rs7996151	0.83[EUR][1000 genomes]
rs9316426	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9316428	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9316429	1.00[YRI][hapmap]
rs9526518	0.85[CEU][hapmap];0.82[CHD][hapmap]
rs9526520	0.84[YRI][hapmap]
rs9535136	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9535145	0.85[CEU][hapmap]
rs9535146	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9535147	0.90[CEU][hapmap];0.86[YRI][hapmap]
rs9535149	0.83[CEU][hapmap]
rs9535154	0.85[CEU][hapmap]
rs9535155	0.85[CEU][hapmap]
rs9535156	0.90[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535166	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9535167	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs9562866	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9562870	0.90[CEU][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];0.87[MKK][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9568150	0.85[CEU][hapmap];0.93[CHD][hapmap]
rs9568151	0.84[CEU][hapmap]
rs9568169	0.80[GIH][hapmap]
rs972297	0.85[CEU][hapmap]

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

No data

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	chr13:49737800-49788800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:49738000-49777000	Weak transcription	Small Intestine	intestine
4	chr13:49738400-49785200	Strong transcription	Liver	Liver
5	chr13:49738600-49785000	Strong transcription	Dnd41	blood
6	chr13:49739600-49786400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:49740200-49786000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:49740400-49784800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr13:49740600-49786600	Strong transcription	Placenta	Placenta
10	chr13:49741600-49783400	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr13:49742600-49783400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:49745600-49783400	Strong transcription	Duodenum Mucosa	Duodenum
13	chr13:49748800-49790600	Weak transcription	K562	blood
14	chr13:49753200-49787600	Weak transcription	Psoas Muscle	Psoas
15	chr13:49756600-49785400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:49756600-49786400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:49756800-49782800	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:49757800-49774600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:49759000-49776200	Weak transcription	Fetal Heart	heart
20	chr13:49759400-49785000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:49759600-49774600	Strong transcription	Adipose Nuclei	Adipose
22	chr13:49759600-49783400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:49759800-49783000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:49759800-49783200	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr13:49760000-49783400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr13:49760000-49785000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:49762800-49789200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:49763000-49788600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr13:49763400-49789200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr13:49764000-49782600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr13:49764400-49783400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr13:49765600-49793800	Weak transcription	A549	lung
33	chr13:49767600-49782200	Weak transcription	Fetal Brain Male	brain
34	chr13:49768600-49786600	Strong transcription	HSMM	muscle
35	chr13:49769000-49781800	Strong transcription	GM12878-XiMat	blood
36	chr13:49769800-49782800	Strong transcription	Fetal Intestine Large	intestine
37	chr13:49769800-49783000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:49769800-49785400	Strong transcription	Fetal Thymus	thymus
39	chr13:49770000-49783600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:49770000-49784800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr13:49770400-49775200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:49770600-49785000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:49770800-49783800	Strong transcription	HUVEC	blood vessel
44	chr13:49771000-49774600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:49771000-49774600	Strong transcription	NHDF-Ad	bronchial
46	chr13:49771000-49774600	Strong transcription	Osteobl	bone
47	chr13:49771000-49782000	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr13:49771000-49782800	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:49771000-49783200	Strong transcription	Primary B cells from cord blood	blood
50	chr13:49771000-49786600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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