Variant report

Variant	rs2742323
Chromosome Location	chr15:72116778-72116779
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:72114514..72117570-chr15:72121768..72126233,5	K562	blood:
2	chr15:72114756..72117570-chr15:72121348..72123847,3	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10518979	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1074330	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11072338	0.87[EUR][1000 genomes]
rs11072339	0.84[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11852789	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11853268	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12439494	0.83[CEU][hapmap]
rs12592364	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12593134	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12595228	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12595464	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12899485	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12901580	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12902006	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12903484	0.87[EUR][1000 genomes]
rs12903980	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906711	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908300	0.80[EUR][1000 genomes]
rs12911154	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913042	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12914070	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12916694	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12916951	0.94[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12917428	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1384007	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956241	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16956273	0.88[CEU][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs16956302	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16956328	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16956381	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16956444	0.87[EUR][1000 genomes]
rs16956452	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2035379	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2054601	0.87[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2200056	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2246225	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279283	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291278	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2306488	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2306490	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2415130	0.82[AMR][1000 genomes]
rs2625529	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs2625530	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723342	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2723343	0.90[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2723356	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2899773	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2957725	0.83[CEU][hapmap]
rs2957737	0.83[CEU][hapmap]
rs34085279	0.87[AMR][1000 genomes]
rs34137768	0.86[EUR][1000 genomes]
rs34514871	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35021156	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35115747	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3784309	0.93[CEU][hapmap];0.84[GIH][hapmap];0.88[JPT][hapmap]
rs4131630	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4238447	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4445848	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4776579	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4776581	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4776584	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4777464	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4777467	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4777469	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4777471	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4777474	0.81[ASN][1000 genomes]
rs4777477	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4777478	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4777480	0.85[EUR][1000 genomes]
rs62023342	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62025574	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6494975	0.83[CEU][hapmap]
rs71395051	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7170461	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7170754	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7177242	0.83[CEU][hapmap]
rs8025504	0.87[EUR][1000 genomes]
rs8028532	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8032038	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8747	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9120	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs972028	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs972029	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs982752	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer 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	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2742323	SENP8	cis	cerebellum	SCAN
rs2742323	TIPIN	cis	parietal	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain
2	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
3	chr15:72110600-72118200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
6	chr15:72112800-72118000	ZNF genes & repeats	Liver	Liver
7	chr15:72113000-72118600	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:72113000-72118800	Weak transcription	Dnd41	blood
9	chr15:72113600-72117000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr15:72113800-72116800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:72114000-72116800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:72114000-72117000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:72114000-72117400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:72114200-72117000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:72114200-72118600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr15:72114200-72118800	Weak transcription	Colonic Mucosa	Colon
17	chr15:72114200-72123200	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr15:72114400-72117000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr15:72114400-72117000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:72114400-72118000	Weak transcription	Brain Germinal Matrix	brain
21	chr15:72114400-72118600	Weak transcription	Brain Anterior Caudate	brain
22	chr15:72114600-72118000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:72114600-72118000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:72114600-72118000	Weak transcription	Fetal Kidney	kidney
25	chr15:72114600-72118600	Weak transcription	Brain Angular Gyrus	brain
26	chr15:72114600-72118600	Weak transcription	Gastric	stomach
27	chr15:72114600-72118800	Weak transcription	Brain Substantia Nigra	brain
28	chr15:72114600-72122600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr15:72114600-72124200	Strong transcription	Placenta	Placenta
30	chr15:72114600-72190600	Weak transcription	Pancreas	Pancrea
31	chr15:72114800-72118400	Weak transcription	NHLF	lung
32	chr15:72114800-72118600	Weak transcription	Fetal Intestine Small	intestine
33	chr15:72114800-72118800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr15:72114800-72122600	Strong transcription	Primary T cells from cord blood	blood
35	chr15:72114800-72124600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:72115000-72118400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:72115000-72118600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:72115200-72118600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:72115200-72123000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:72115400-72117200	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr15:72115400-72118000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr15:72115400-72118600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr15:72115400-72118600	Weak transcription	Thymus	Thymus
44	chr15:72115400-72122800	Strong transcription	HSMM	muscle
45	chr15:72115600-72117600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr15:72115600-72118000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:72115600-72118400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:72115600-72118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:72115600-72118600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:72115600-72118800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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