Variant report

Variant	rs8747
Chromosome Location	chr15:72115541-72115542
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:72114514..72117570-chr15:72121768..72126233,5	K562	blood:
2	chr15:72100596..72102959-chr15:72114173..72115754,2	MCF-7	breast:
3	chr15:72114756..72117570-chr15:72121348..72123847,3	K562	blood:
4	chr15:72114725..72116485-chr15:72127394..72129983,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRAMD2-6	chr15:72114640-72115963	NONHSAT047051

Variant related genes	Relation type
ENSG00000031544	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1074330	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap]
rs11072332	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11072339	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.80[AMR][1000 genomes]
rs12899485	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902006	0.87[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap]
rs12903980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12906711	0.86[AMR][1000 genomes]
rs12911154	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12913042	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12916951	0.87[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs12917428	0.86[AMR][1000 genomes]
rs1384007	0.85[AMR][1000 genomes]
rs16956241	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16956273	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs16956302	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16956328	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16956381	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2054601	0.80[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap]
rs2246225	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291278	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2306490	0.86[AMR][1000 genomes]
rs2625529	0.87[CEU][hapmap];0.82[CHB][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs2625530	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2723342	0.86[CEU][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2723343	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2723356	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2742323	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]
rs34085279	0.81[AMR][1000 genomes]
rs34514871	0.87[AMR][1000 genomes]
rs35021156	0.89[AMR][1000 genomes]
rs3784309	1.00[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap]
rs4238447	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4776579	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4776581	0.86[AMR][1000 genomes]
rs4777464	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777467	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4777471	0.84[AMR][1000 genomes]
rs62023342	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs62025574	0.86[AMR][1000 genomes]
rs71395051	0.81[AMR][1000 genomes]
rs7170461	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs7170754	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs8178	0.82[CEU][hapmap]
rs9120	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972028	0.80[EUR][1000 genomes]
rs972029	0.80[EUR][1000 genomes]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs8747	TIPIN	cis	parietal	SCAN
rs8747	SENP8	cis	cerebellum	SCAN
rs8747	PARP6	cis	parietal	SCAN
rs8747	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72107800-72115600	Weak transcription	Fetal Heart	heart
2	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain
3	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
4	chr15:72110600-72118200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:72110800-72116400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr15:72111600-72116600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
8	chr15:72111800-72116400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:72112000-72115800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:72112000-72116200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
12	chr15:72112800-72118000	ZNF genes & repeats	Liver	Liver
13	chr15:72113000-72116000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:72113000-72118600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:72113000-72118800	Weak transcription	Dnd41	blood
16	chr15:72113600-72117000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:72113800-72115600	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr15:72113800-72115800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
19	chr15:72113800-72116400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr15:72113800-72116400	ZNF genes & repeats	Left Ventricle	heart
21	chr15:72113800-72116400	ZNF genes & repeats	NH-A	brain
22	chr15:72113800-72116400	ZNF genes & repeats	NHEK	skin
23	chr15:72113800-72116600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr15:72113800-72116800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:72114000-72115600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:72114000-72115600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr15:72114000-72115600	ZNF genes & repeats	Osteobl	bone
28	chr15:72114000-72115800	Strong transcription	Fetal Intestine Large	intestine
29	chr15:72114000-72116200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:72114000-72116200	ZNF genes & repeats	Adipose Nuclei	Adipose
31	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
32	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:72114000-72116400	Strong transcription	Rectal Smooth Muscle	rectum
34	chr15:72114000-72116800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:72114000-72117000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr15:72114000-72117400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr15:72114200-72115600	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
38	chr15:72114200-72115800	ZNF genes & repeats	Primary B cells from cord blood	blood
39	chr15:72114200-72115800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
40	chr15:72114200-72116400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
41	chr15:72114200-72116400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
42	chr15:72114200-72116400	ZNF genes & repeats	Aorta	Aorta
43	chr15:72114200-72116400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
44	chr15:72114200-72116400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
45	chr15:72114200-72116400	ZNF genes & repeats	HMEC	breast
46	chr15:72114200-72117000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr15:72114200-72118600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr15:72114200-72118800	Weak transcription	Colonic Mucosa	Colon
49	chr15:72114200-72123200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr15:72114400-72115800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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