Variant report

Variant	rs1703768
Chromosome Location	chr15:99693682-99693683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99677279..99681777-chr15:99693510..99696751,5	MCF-7	breast:
2	chr15:99688236..99691160-chr15:99691994..99693833,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261616	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12915090	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1318292	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1670213	0.93[AFR][1000 genomes]
rs1670216	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1670221	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1703763	0.94[AFR][1000 genomes]
rs1703766	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs1703767	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs187755	0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs2602021	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602022	0.92[AFR][1000 genomes]
rs2602029	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602034	0.90[CHB][hapmap]
rs2623180	0.88[EUR][1000 genomes]
rs2623181	0.89[EUR][1000 genomes]
rs2623193	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4965445	0.83[CEU][hapmap]
rs7167303	0.86[CHB][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1703768	RP11-6O2.4	cis	Adipose Subcutaneous	GTEx
rs1703768	SYNM	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99665000-99714200	Weak transcription	NHEK	skin
2	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
3	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
4	chr15:99676200-99696200	Weak transcription	NH-A	brain
5	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
6	chr15:99676800-99694400	Weak transcription	HUVEC	blood vessel
7	chr15:99677600-99695200	Weak transcription	Hela-S3	cervix
8	chr15:99677800-99696200	Weak transcription	HMEC	breast
9	chr15:99678200-99696400	Weak transcription	Placenta	Placenta
10	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr15:99679800-99696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:99679800-99696200	Weak transcription	Esophagus	oesophagus
13	chr15:99684200-99694400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:99684400-99694000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:99684400-99696200	Weak transcription	HepG2	liver
16	chr15:99684600-99694000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr15:99684600-99694400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:99684600-99694400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:99684600-99694600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr15:99684600-99695600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:99684600-99695800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr15:99684600-99695800	Weak transcription	Osteobl	bone
23	chr15:99684600-99698800	Weak transcription	Aorta	Aorta
24	chr15:99684600-99706600	Weak transcription	Right Atrium	heart
25	chr15:99684800-99709200	Weak transcription	Colonic Mucosa	Colon
26	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:99685000-99697800	Weak transcription	NHDF-Ad	bronchial
28	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:99688600-99697000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:99688800-99694600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:99689400-99695800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:99689400-99699800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr15:99689600-99694400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:99689600-99699000	Weak transcription	Dnd41	blood
35	chr15:99689600-99707600	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:99689600-99709600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:99689800-99696400	Weak transcription	Psoas Muscle	Psoas
38	chr15:99689800-99697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr15:99689800-99699400	Weak transcription	Brain Substantia Nigra	brain
40	chr15:99689800-99703400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:99689800-99709400	Weak transcription	Brain Angular Gyrus	brain
42	chr15:99690000-99708200	Weak transcription	Right Ventricle	heart
43	chr15:99690000-99709400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:99690200-99697800	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:99690200-99699000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:99690200-99699000	Weak transcription	A549	lung
47	chr15:99690200-99704800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:99690400-99694400	Weak transcription	Fetal Lung	lung
49	chr15:99690400-99705400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:99690400-99706600	Weak transcription	Spleen	Spleen

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