Variant report

Variant	rs7172665
Chromosome Location	chr15:83717146-83717147
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:83714861..83717346-chr15:83721715..83724046,2	K562	blood:
2	chr15:83715559..83717432-chr15:83875352..83877584,2	MCF-7	breast:
3	chr15:83710008..83713519-chr15:83714688..83717588,4	K562	blood:
4	chr15:83715424..83718064-chr15:83719632..83721624,3	K562	blood:
5	chr15:83712893..83715899-chr15:83717141..83719784,3	MCF-7	breast:
6	chr15:83712066..83714365-chr15:83715736..83718264,3	MCF-7	breast:
7	chr15:83715424..83717754-chr15:83719632..83721290,2	K562	blood:
8	chr15:83716790..83719307-chr15:83732798..83735567,2	MCF-7	breast:
9	chr15:83711130..83713697-chr15:83715382..83717588,2	K562	blood:
10	chr15:83678274..83681051-chr15:83713533..83717872,4	MCF-7	breast:
11	chr15:83714522..83717399-chr15:83720662..83723251,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259308	Chromatin interaction
ENSG00000169609	Chromatin interaction
ENSG00000064726	Chromatin interaction
ENSG00000166503	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10400812	0.96[CEU][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12439782	0.90[EUR][1000 genomes]
rs12899522	0.92[EUR][1000 genomes]
rs12904695	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12906626	0.89[EUR][1000 genomes]
rs12907032	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12913130	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13329195	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13329269	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2084839	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2381030	1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28580677	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs3087804	0.96[CEU][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4079029	0.87[ASW][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs61375537	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6603044	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6603046	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7163516	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7166645	0.86[EUR][1000 genomes]
rs7170547	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7177599	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7181169	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs750214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8023669	0.96[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap]
rs8040457	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8040998	1.00[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040336	chr15:83578947-83768335	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers 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	38 gene(s)	inside rSNPs	diseases
2	nsv482308	chr15:83584918-83747362	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers 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	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7172665	TM6SF1	cis	cerebellum	SCAN
rs7172665	HDGFRP3	Cis_1M	lymphoblastoid	RTeQTL
rs7172665	BTBD1	cis	parietal	SCAN
rs7172665	WHAMM	cis	cerebellum	SCAN
rs7172665	WHAMM	cis	parietal	SCAN
rs7172665	ARNT2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83681600-83732000	Weak transcription	Stomach Mucosa	stomach
2	chr15:83683000-83723000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:83683400-83726600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:83697800-83721000	Strong transcription	Fetal Intestine Large	intestine
5	chr15:83699000-83725800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:83700400-83734400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:83701600-83732800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:83705000-83720800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:83705000-83725800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:83705000-83731000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr15:83705200-83720000	Strong transcription	Dnd41	blood
12	chr15:83705600-83721400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:83706000-83725400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:83706600-83718000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr15:83706800-83726600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:83707000-83725400	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:83707400-83718400	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:83707400-83725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:83707800-83719200	Strong transcription	GM12878-XiMat	blood
20	chr15:83708000-83718000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:83708000-83718200	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr15:83708000-83722000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:83708000-83725400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:83708600-83719800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr15:83708600-83726000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr15:83708800-83726400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:83708800-83726600	Weak transcription	Pancreas	Pancrea
28	chr15:83709000-83726600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:83709000-83726600	Weak transcription	Fetal Brain Male	brain
30	chr15:83709200-83724400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:83709200-83727000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr15:83709600-83730800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr15:83710400-83722800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:83710600-83717200	Weak transcription	Ovary	ovary
35	chr15:83710600-83717800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:83710600-83722000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:83710600-83723800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr15:83710600-83723800	Weak transcription	Brain Angular Gyrus	brain
39	chr15:83710600-83730200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:83710600-83730200	Weak transcription	Esophagus	oesophagus
41	chr15:83710800-83717400	Weak transcription	Osteobl	bone
42	chr15:83710800-83725800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr15:83711400-83720800	Strong transcription	K562	blood
44	chr15:83711600-83719800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:83711800-83724800	Strong transcription	Hela-S3	cervix
46	chr15:83711800-83725000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:83712000-83719000	Strong transcription	Placenta	Placenta
48	chr15:83712200-83720000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:83712200-83725800	Weak transcription	Right Ventricle	heart
50	chr15:83712400-83722600	Weak transcription	Brain Germinal Matrix	brain

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