Variant report

Variant	rs7161889
Chromosome Location	chr15:58983425-58983426
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58982751..58984795-chr15:59030172..59031707,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLTM-6	chr15:58982672-58985806	NR_073415

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10152558	0.83[CHB][hapmap]
rs11071398	0.95[YRI][hapmap]
rs11638244	0.93[YRI][hapmap]
rs11854073	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12439457	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899638	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12911832	0.88[ASN][1000 genomes]
rs12911961	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12912003	0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12912699	0.83[AFR][1000 genomes]
rs1427281	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.88[ASN][1000 genomes]
rs1427282	0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1648532	1.00[CHB][hapmap];0.86[YRI][hapmap]
rs17269397	0.83[CHB][hapmap]
rs1834747	0.87[ASN][1000 genomes]
rs2555356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2657125	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs28864995	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs347115	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs347117	1.00[ASW][hapmap];0.96[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs383902	1.00[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs387812	1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[YRI][hapmap]
rs442495	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs474875	0.83[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs4774310	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4775086	0.83[GIH][hapmap];0.82[MKK][hapmap]
rs4775087	1.00[ASW][hapmap];0.96[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];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4775094	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap]
rs507801	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs514049	0.83[GIH][hapmap]
rs593742	0.93[GIH][hapmap];0.88[MEX][hapmap]
rs596379	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs605928	0.91[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap]
rs610877	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs6494029	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6494035	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6494036	0.83[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6494037	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs653765	0.92[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[ASN][1000 genomes]
rs673813	1.00[CHB][hapmap]
rs714696	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7163162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171818	0.81[CHB][hapmap]
rs7177678	0.83[GIH][hapmap]
rs7183336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8043406	0.81[GIH][hapmap];0.82[MKK][hapmap]
rs972801	0.92[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
5	nsv974583	chr15:58979010-58987450	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:58936200-58991400	Weak transcription	HMEC	breast
3	chr15:58951200-58987000	Weak transcription	NHEK	skin
4	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:58956600-58984400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:58957400-58984400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr15:58961800-58984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
16	chr15:58968200-58984000	Weak transcription	Brain Germinal Matrix	brain
17	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
18	chr15:58969200-58984200	Weak transcription	Fetal Intestine Large	intestine
19	chr15:58970600-58987200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:58971800-58984800	Weak transcription	NHDF-Ad	bronchial
21	chr15:58971800-58986800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:58972000-58986600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:58972400-58984200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr15:58972600-58984400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:58972600-58984400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:58972600-58988400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr15:58972600-58988800	Weak transcription	Fetal Stomach	stomach
28	chr15:58972600-58989000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:58973200-58984600	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr15:58973200-58984800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:58973600-58984200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:58974600-58991000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr15:58975800-58989200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:58976800-58984200	Weak transcription	Fetal Muscle Leg	muscle
35	chr15:58976800-58986400	Weak transcription	Gastric	stomach
36	chr15:58976800-58986600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr15:58977000-58984200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr15:58977000-58984400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:58977000-58984400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:58977000-58984800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:58977000-58988600	Weak transcription	Fetal Intestine Small	intestine
42	chr15:58977000-58989000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr15:58977200-58983600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:58977200-58983600	Weak transcription	GM12878-XiMat	blood
45	chr15:58977200-58984200	Weak transcription	A549	lung
46	chr15:58977200-58984400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:58977200-58984400	Weak transcription	Liver	Liver
48	chr15:58977200-58984800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:58977200-58984800	Weak transcription	Hela-S3	cervix
50	chr15:58977200-58986600	Weak transcription	Stomach Mucosa	stomach

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