Variant report

Variant	rs1712407
Chromosome Location	chr15:42487299-42487300
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	JUN	chr15:42486631-42487445	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42443129..42444925-chr15:42485873..42487790,2	MCF-7	breast:
2	chr15:42482969..42485392-chr15:42485686..42487321,2	MCF-7	breast:

Variant related genes	Relation type
VPS39	TF binding region
ENSG00000166887	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs10152909	0.84[ASN][1000 genomes]
rs10518763	1.00[CEU][hapmap]
rs11070363	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs12324804	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12440779	0.81[ASN][1000 genomes]
rs12442769	0.84[ASN][1000 genomes]
rs12915387	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12915946	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs12917071	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs1616957	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1619537	0.92[ASN][1000 genomes]
rs1626437	1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1630294	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs1659215	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs1678987	0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs1678988	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[ASN][1000 genomes]
rs1678989	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs1678990	0.88[ASN][1000 genomes]
rs1678995	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.98[ASN][1000 genomes]
rs1678996	0.98[ASN][1000 genomes]
rs1679000	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1679001	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1679011	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs16973053	1.00[CEU][hapmap]
rs16973054	1.00[CEU][hapmap]
rs16973059	1.00[CEU][hapmap]
rs16973089	1.00[CEU][hapmap]
rs16973091	1.00[CEU][hapmap]
rs16973093	1.00[CEU][hapmap]
rs16973095	1.00[CEU][hapmap]
rs16973096	1.00[CEU][hapmap]
rs16973097	1.00[CEU][hapmap]
rs16973107	1.00[CEU][hapmap]
rs16973109	1.00[CEU][hapmap]
rs16973132	1.00[CEU][hapmap]
rs16973137	1.00[CEU][hapmap]
rs16973148	1.00[CEU][hapmap]
rs16973153	1.00[CEU][hapmap]
rs16973155	1.00[CEU][hapmap]
rs16973171	1.00[CEU][hapmap]
rs16973174	1.00[CEU][hapmap]
rs16973175	1.00[CEU][hapmap]
rs1703748	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs1703751	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1703753	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712390	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1712391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1712397	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs1712406	0.92[ASN][1000 genomes]
rs1712408	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs1712409	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs1712410	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1712417	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1712420	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs1712422	0.92[ASN][1000 genomes]
rs1712442	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17695121	1.00[CEU][hapmap]
rs1801449	0.82[CEU][hapmap]
rs2412671	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2412674	0.92[ASN][1000 genomes]
rs2412704	1.00[CEU][hapmap]
rs2620378	0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2620379	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2620380	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs2620381	0.90[ASN][1000 genomes]
rs2620383	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2620387	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs2663092	0.98[ASN][1000 genomes]
rs2663093	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2663096	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2677751	0.98[ASN][1000 genomes]
rs28364347	1.00[CEU][hapmap]
rs28767320	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2928333	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4344713	1.00[CEU][hapmap]
rs4583208	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs4923934	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs4923935	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4923937	0.86[YRI][hapmap]
rs4924633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4924635	0.84[ASN][1000 genomes]
rs4924636	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4924638	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924642	0.88[YRI][hapmap]
rs4924643	0.81[YRI][hapmap]
rs583541	0.94[ASN][1000 genomes]
rs588695	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs590540	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593910	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs598441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599316	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs602270	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs603468	0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs607959	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs609660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613090	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[ASN][1000 genomes]
rs613131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs613157	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs614733	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs614774	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs615023	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[ASN][1000 genomes]
rs616071	0.98[ASN][1000 genomes]
rs618161	0.92[ASN][1000 genomes]
rs621365	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs627478	0.98[ASN][1000 genomes]
rs629255	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[ASN][1000 genomes]
rs633310	0.88[ASN][1000 genomes]
rs633483	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635669	0.98[ASN][1000 genomes]
rs635690	0.98[ASN][1000 genomes]
rs635919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636604	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs637445	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[ASN][1000 genomes]
rs638240	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs641119	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644627	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs645304	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs647581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648720	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[ASN][1000 genomes]
rs6493026	0.89[YRI][hapmap]
rs650910	0.98[ASN][1000 genomes]
rs652192	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs659354	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs660033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs663454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665262	0.98[ASN][1000 genomes]
rs665718	0.98[ASN][1000 genomes]
rs668973	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs670329	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs670421	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs672946	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs677845	0.85[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs677895	0.98[ASN][1000 genomes]
rs683227	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs683579	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs685521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164437	1.00[CEU][hapmap]
rs7164874	1.00[CEU][hapmap]
rs7165023	1.00[CEU][hapmap]
rs7170943	0.85[YRI][hapmap]
rs7178901	1.00[CEU][hapmap]
rs7181577	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182797	1.00[CEU][hapmap]
rs8023923	0.92[ASN][1000 genomes]
rs8030650	0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs8031735	0.85[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8036917	0.84[ASN][1000 genomes]
rs8037100	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs8038153	1.00[CEU][hapmap]
rs8108	0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9783720	0.84[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	nsv471683	chr15:42334375-42502982	Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Weak transcription 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1712407	LRRC57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42450600-42487400	Strong transcription	Primary B cells from cord blood	blood
2	chr15:42451000-42487600	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:42451200-42487600	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:42460000-42499200	Weak transcription	A549	lung
5	chr15:42460000-42499800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:42466000-42498800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:42475000-42499200	Weak transcription	Stomach Mucosa	stomach
8	chr15:42476800-42499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:42477200-42497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:42477400-42487400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:42478400-42498600	Weak transcription	Gastric	stomach
12	chr15:42480200-42496000	Weak transcription	Esophagus	oesophagus
13	chr15:42480400-42498600	Weak transcription	Small Intestine	intestine
14	chr15:42480400-42498800	Weak transcription	Right Ventricle	heart
15	chr15:42480600-42491400	Weak transcription	Psoas Muscle	Psoas
16	chr15:42480600-42496000	Weak transcription	Spleen	Spleen
17	chr15:42481200-42499800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:42481400-42489600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:42481600-42497600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr15:42481600-42497600	Weak transcription	HUVEC	blood vessel
21	chr15:42481600-42498600	Weak transcription	Fetal Brain Male	brain
22	chr15:42482800-42499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:42483200-42499400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr15:42483400-42489600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:42483400-42498600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:42483400-42498600	Weak transcription	Fetal Kidney	kidney
27	chr15:42483600-42497600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:42483600-42498600	Weak transcription	Brain Substantia Nigra	brain
29	chr15:42483600-42498600	Weak transcription	K562	blood
30	chr15:42483600-42499200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr15:42483800-42489600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:42483800-42489600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr15:42483800-42489600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:42483800-42489600	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:42483800-42492600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr15:42483800-42499400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:42484000-42489600	Weak transcription	Placenta	Placenta
38	chr15:42484000-42489800	Weak transcription	NHDF-Ad	bronchial
39	chr15:42484000-42499200	Weak transcription	HMEC	breast
40	chr15:42484200-42489600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:42484200-42490000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:42484200-42491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:42484200-42493400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:42484400-42489600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:42484400-42489600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr15:42484400-42489600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr15:42484400-42489600	Weak transcription	NH-A	brain
48	chr15:42484400-42489800	Weak transcription	HSMM	muscle
49	chr15:42484400-42490000	Weak transcription	Ovary	ovary
50	chr15:42484400-42495800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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