Variant report

Variant	rs1712422
Chromosome Location	chr15:42511119-42511120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42498997..42501611-chr15:42508533..42512053,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GANC-1	chr15:42511117-42511151	ENSG00000261002.1

Variant related genes	Relation type
ENSG00000166887	Chromatin interaction
ENSG00000261002	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10152909	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070363	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11070368	0.85[AFR][1000 genomes]
rs11858453	0.85[AFR][1000 genomes]
rs12324804	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12440779	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12442769	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913755	0.85[AFR][1000 genomes]
rs12915387	0.96[ASN][1000 genomes]
rs12915946	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917071	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1616957	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1619537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1626437	0.94[ASN][1000 genomes]
rs1630294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678987	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1678995	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678996	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679000	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1679001	0.92[ASN][1000 genomes]
rs1679008	0.92[ASN][1000 genomes]
rs1679011	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1703748	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1703751	0.90[ASN][1000 genomes]
rs1703753	0.92[ASN][1000 genomes]
rs1712390	0.94[ASN][1000 genomes]
rs1712391	0.92[ASN][1000 genomes]
rs1712397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712406	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712407	0.92[ASN][1000 genomes]
rs1712408	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1712409	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1712410	0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1712417	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1712420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1712442	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2412671	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2412674	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2412677	0.85[AFR][1000 genomes]
rs2412681	0.85[AFR][1000 genomes]
rs2620378	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2620379	0.92[ASN][1000 genomes]
rs2620380	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2620381	0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2620383	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620387	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2663092	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2663096	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2677751	0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28767320	0.88[ASN][1000 genomes]
rs2928333	0.92[ASN][1000 genomes]
rs4923934	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4923937	0.91[AFR][1000 genomes]
rs4924633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924635	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4924636	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4924638	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924640	0.95[AFR][1000 genomes]
rs4924642	0.91[AFR][1000 genomes]
rs4924643	0.95[AFR][1000 genomes]
rs583541	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs588695	0.90[ASN][1000 genomes]
rs590540	0.92[ASN][1000 genomes]
rs593910	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs598441	0.90[ASN][1000 genomes]
rs602270	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs603468	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs607959	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609660	0.90[ASN][1000 genomes]
rs613090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613131	0.90[ASN][1000 genomes]
rs613157	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614733	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs614774	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs615023	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs616071	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618161	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs621365	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627478	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs629255	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs633310	0.96[ASN][1000 genomes]
rs633483	0.92[ASN][1000 genomes]
rs635617	0.92[ASN][1000 genomes]
rs635669	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs635690	0.94[ASN][1000 genomes]
rs635919	0.92[ASN][1000 genomes]
rs636604	0.94[ASN][1000 genomes]
rs637445	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs638240	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs641119	0.92[ASN][1000 genomes]
rs644627	0.94[ASN][1000 genomes]
rs645304	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs647581	0.92[ASN][1000 genomes]
rs648720	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493026	0.95[AFR][1000 genomes]
rs6493028	0.85[AFR][1000 genomes]
rs6493029	0.85[AFR][1000 genomes]
rs650910	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs652192	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659354	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs660033	0.92[ASN][1000 genomes]
rs663454	0.92[ASN][1000 genomes]
rs665262	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs665718	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs668973	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670329	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670421	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs672946	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67384392	0.93[AFR][1000 genomes]
rs677845	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs677895	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs683227	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683579	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs685521	0.92[ASN][1000 genomes]
rs7164480	0.96[AFR][1000 genomes]
rs7164484	0.82[AFR][1000 genomes]
rs7170943	0.95[AFR][1000 genomes]
rs7181577	0.92[ASN][1000 genomes]
rs8023923	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8030650	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8031735	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036917	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8108	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783720	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh 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	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS 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	12 gene(s)	inside rSNPs	diseases
6	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500600-42513800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
3	chr15:42501000-42512600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:42501000-42512800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:42501000-42513600	Strong transcription	HSMM	muscle
6	chr15:42501000-42518600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:42501000-42518800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:42501000-42520800	Weak transcription	Psoas Muscle	Psoas
9	chr15:42501000-42534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:42501000-42536600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:42501000-42536800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:42501000-42538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr15:42501200-42513000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:42501200-42514200	Weak transcription	Right Ventricle	heart
15	chr15:42501200-42514600	Weak transcription	Pancreas	Pancrea
16	chr15:42501200-42523200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:42501200-42532400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr15:42501400-42512600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:42501400-42512800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:42501400-42513000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:42501600-42512600	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr15:42501600-42512800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:42501600-42513000	Strong transcription	Liver	Liver
24	chr15:42501800-42536800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:42502000-42511400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:42502000-42512600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:42502000-42512800	Strong transcription	Osteobl	bone
28	chr15:42502000-42521200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:42502000-42535000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr15:42502200-42512200	Strong transcription	Primary T cells from cord blood	blood
31	chr15:42502200-42512600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:42502200-42512800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:42502200-42512800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:42502200-42512800	Strong transcription	NH-A	brain
35	chr15:42502200-42512800	Strong transcription	NHDF-Ad	bronchial
36	chr15:42502200-42513000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr15:42502200-42534000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr15:42502200-42536600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:42502400-42512600	Strong transcription	Dnd41	blood
40	chr15:42502400-42519600	Strong transcription	Fetal Intestine Large	intestine
41	chr15:42502800-42512600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr15:42502800-42535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:42502800-42536400	Strong transcription	Fetal Muscle Leg	muscle
44	chr15:42503200-42512200	Strong transcription	Adipose Nuclei	Adipose
45	chr15:42503200-42517600	Weak transcription	Gastric	stomach
46	chr15:42503200-42544000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:42504000-42511400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:42504000-42516200	Weak transcription	Esophagus	oesophagus
49	chr15:42504000-42516200	Weak transcription	A549	lung
50	chr15:42504000-42517800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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