Variant report

Variant	rs7164548
Chromosome Location	chr15:99666329-99666330
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99644993..99646793-chr15:99665159..99667351,2	MCF-7	breast:
2	chr15:99665709..99667621-chr15:99675687..99677257,2	K562	blood:
3	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259475	Chromatin interaction
ENSG00000182253	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12324825	0.86[CHB][hapmap]
rs12591477	0.87[CHB][hapmap]
rs12595457	0.80[AMR][1000 genomes]
rs12911794	0.83[ASN][1000 genomes]
rs1810091	0.95[CHB][hapmap]
rs2242076	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs4965445	0.85[CEU][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap]
rs56009713	0.80[ASN][1000 genomes]
rs7162579	0.81[ASN][1000 genomes]
rs7167303	0.84[JPT][hapmap]
rs8032817	0.95[CHB][hapmap]
rs8038392	0.81[CHB][hapmap]
rs8041213	0.85[ASN][1000 genomes]
rs906760	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS 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	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS 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	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7164548	LYSMD4	cis	cerebellum	SCAN
rs7164548	TTC23	cis	multi-tissue	Pritchard
rs7164548	SYNM	cis	cerebellum	SCAN
rs7164548	SYNM	cis	parietal	SCAN
rs7164548	TTC23	cis	parietal	SCAN
rs7164548	TTC23	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
2	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
3	chr15:99660600-99671600	Weak transcription	Liver	Liver
4	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:99663200-99666400	Enhancers	Fetal Brain Male	brain
7	chr15:99663200-99666400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr15:99663200-99666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:99663200-99666800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
10	chr15:99663600-99667000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:99664200-99666800	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:99664200-99667200	Enhancers	Fetal Muscle Leg	muscle
14	chr15:99664200-99675800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr15:99664400-99666400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr15:99664400-99666800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:99664400-99666800	Enhancers	Brain Substantia Nigra	brain
18	chr15:99664400-99667200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:99664400-99667400	Enhancers	Right Atrium	heart
20	chr15:99664400-99678800	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:99664400-99678800	Weak transcription	Brain Germinal Matrix	brain
22	chr15:99664600-99666600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:99664600-99666600	Enhancers	Brain Anterior Caudate	brain
24	chr15:99664600-99667200	Enhancers	Left Ventricle	heart
25	chr15:99664600-99667400	Enhancers	Psoas Muscle	Psoas
26	chr15:99664600-99668800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:99664600-99672600	Weak transcription	Small Intestine	intestine
28	chr15:99664600-99676800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:99664600-99677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:99664600-99678800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr15:99664800-99666600	Enhancers	Brain Hippocampus Middle	brain
33	chr15:99664800-99666800	Enhancers	NH-A	brain
34	chr15:99664800-99667200	Weak transcription	Pancreas	Pancrea
35	chr15:99664800-99669200	Weak transcription	Fetal Lung	lung
36	chr15:99664800-99672800	Weak transcription	Fetal Thymus	thymus
37	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:99665000-99666600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:99665000-99666800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:99665000-99667400	Weak transcription	Fetal Intestine Large	intestine
42	chr15:99665000-99668400	Weak transcription	Fetal Intestine Small	intestine
43	chr15:99665000-99668800	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr15:99665000-99668800	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:99665000-99670000	Weak transcription	Colonic Mucosa	Colon
46	chr15:99665000-99670200	Weak transcription	HepG2	liver
47	chr15:99665000-99676000	Genic enhancers	Colon Smooth Muscle	Colon
48	chr15:99665000-99676600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:99665000-99676800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum

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