Variant report

Variant	rs8178
Chromosome Location	chr15:72114747-72114748
allele	C/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	chr15:72114725..72116485-chr15:72127394..72129983,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THSD4-4	chr15:72114376-72114796	ENSG00000260037.1
2	lnc-GRAMD2-6	chr15:72114640-72115963	NONHSAT047051

Variant related genes	Relation type
ENSG00000031544	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10851847	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11633167	0.83[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11634608	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap]
rs12050794	0.81[AMR][1000 genomes]
rs12439494	0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs12898728	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12898868	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12912771	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1481862	0.81[AMR][1000 genomes]
rs16956273	0.88[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs16956369	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2128112	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2246225	0.82[CEU][hapmap]
rs2306489	0.83[ASN][1000 genomes]
rs2306576	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415120	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2415121	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2415126	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415128	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs2625529	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2723343	0.82[CEU][hapmap]
rs28650442	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs28717020	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2929508	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2929509	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2929510	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2929511	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2930069	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2957724	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2957725	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs2957728	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2957734	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs2957735	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2957737	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3784309	0.83[CEU][hapmap]
rs3784310	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs3784313	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4511483	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4526973	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777466	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62023343	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6494973	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6494975	0.91[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs7173626	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7175373	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7177242	0.82[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs7403191	0.85[ASN][1000 genomes]
rs7496582	0.83[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7497104	0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036307	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8040216	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8557	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8747	0.82[CEU][hapmap]
rs9302260	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs982752	0.82[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8178	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72107200-72115200	Weak transcription	Fetal Stomach	stomach
2	chr15:72107800-72115600	Weak transcription	Fetal Heart	heart
3	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain
4	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
5	chr15:72110600-72118200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:72110800-72116400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:72111600-72116600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
9	chr15:72111800-72116400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:72112000-72115800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:72112000-72116200	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
13	chr15:72112600-72114800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:72112800-72118000	ZNF genes & repeats	Liver	Liver
15	chr15:72113000-72115400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:72113000-72116000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:72113000-72118600	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:72113000-72118800	Weak transcription	Dnd41	blood
19	chr15:72113600-72117000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:72113800-72114800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
21	chr15:72113800-72114800	ZNF genes & repeats	NHDF-Ad	bronchial
22	chr15:72113800-72115400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr15:72113800-72115400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
24	chr15:72113800-72115400	ZNF genes & repeats	Fetal Lung	lung
25	chr15:72113800-72115600	Strong transcription	Placenta Amnion	Placenta Amnion
26	chr15:72113800-72115800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
27	chr15:72113800-72116400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr15:72113800-72116400	ZNF genes & repeats	Left Ventricle	heart
29	chr15:72113800-72116400	ZNF genes & repeats	NH-A	brain
30	chr15:72113800-72116400	ZNF genes & repeats	NHEK	skin
31	chr15:72113800-72116600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr15:72113800-72116800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:72114000-72114800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr15:72114000-72114800	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
35	chr15:72114000-72115000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:72114000-72115200	Weak transcription	Small Intestine	intestine
37	chr15:72114000-72115400	ZNF genes & repeats	HSMM	muscle
38	chr15:72114000-72115600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
39	chr15:72114000-72115600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
40	chr15:72114000-72115600	ZNF genes & repeats	Osteobl	bone
41	chr15:72114000-72115800	Strong transcription	Fetal Intestine Large	intestine
42	chr15:72114000-72116200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:72114000-72116200	ZNF genes & repeats	Adipose Nuclei	Adipose
44	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr15:72114000-72116400	Strong transcription	Rectal Smooth Muscle	rectum
47	chr15:72114000-72116800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:72114000-72117000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr15:72114000-72117400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:72114200-72114800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast

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