Variant report

Variant	rs7162949
Chromosome Location	chr15:99798934-99798935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99791300..99794285-chr15:99798721..99800765,2	K562	blood:

Variant related genes	Relation type
ENSG00000168904	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1033036	0.86[YRI][hapmap]
rs10794475	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10902543	0.81[YRI][hapmap]
rs10902544	0.87[YRI][hapmap]
rs11853278	0.89[YRI][hapmap]
rs12592075	0.86[YRI][hapmap]
rs12906357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913897	0.82[YRI][hapmap]
rs1876927	0.86[YRI][hapmap]
rs2089709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136627	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4965225	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6598229	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6598230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6598237	0.86[YRI][hapmap]
rs7168227	0.82[YRI][hapmap]
rs7169906	0.82[YRI][hapmap]
rs7171205	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171210	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171217	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7182425	0.89[YRI][hapmap]
rs7182675	0.86[YRI][hapmap]
rs8040850	0.86[YRI][hapmap]
rs8041923	0.82[YRI][hapmap]
rs8042249	0.86[YRI][hapmap]
rs8042667	0.86[YRI][hapmap]
rs9920227	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920437	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
15	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats 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	47 gene(s)	inside rSNPs	diseases
18	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
19	nsv977759	chr15:99798851-99799851	Weak transcription Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7162949	SYNM	cis	parietal	SCAN
rs7162949	TTC23	cis	parietal	SCAN
rs7162949	NR2F2	cis	parietal	SCAN
rs7162949	TTC23	cis	multi-tissue	Pritchard
rs7162949	TTC23	cis	cerebellum	SCAN
rs7162949	TTC23	cis	lymphoblastoid	seeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99792200-99802800	Weak transcription	Esophagus	oesophagus
2	chr15:99792200-99807400	Weak transcription	Ovary	ovary
3	chr15:99792200-99846400	Weak transcription	Lung	lung
4	chr15:99792400-99804200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:99792600-99832200	Weak transcription	Aorta	Aorta
6	chr15:99792800-99801600	Weak transcription	Fetal Stomach	stomach
7	chr15:99792800-99802800	Weak transcription	A549	lung
8	chr15:99792800-99804200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:99792800-99804600	Weak transcription	Placenta	Placenta
10	chr15:99792800-99847000	Weak transcription	Right Ventricle	heart
11	chr15:99793000-99799000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:99793000-99799400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:99793000-99803200	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:99793000-99804200	Weak transcription	Fetal Heart	heart
15	chr15:99793000-99804400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:99793000-99804600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:99793000-99805400	Weak transcription	Fetal Brain Female	brain
18	chr15:99793000-99823800	Weak transcription	Fetal Brain Male	brain
19	chr15:99793000-99838000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:99793000-99850400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr15:99793000-99866600	Weak transcription	Gastric	stomach
22	chr15:99793200-99804200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr15:99793200-99805600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:99793200-99805800	Weak transcription	Brain Germinal Matrix	brain
25	chr15:99793200-99808000	Weak transcription	Fetal Kidney	kidney
26	chr15:99793200-99822400	Weak transcription	Adipose Nuclei	Adipose
27	chr15:99793400-99803000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr15:99794000-99804200	Weak transcription	Thymus	Thymus
29	chr15:99794000-99804400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr15:99794000-99804400	Weak transcription	Spleen	Spleen
31	chr15:99794000-99805000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:99794000-99808400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:99794000-99830800	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:99794000-99840000	Weak transcription	Brain Anterior Caudate	brain
35	chr15:99794000-99846400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:99794200-99799200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr15:99794200-99799600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr15:99794200-99799600	Weak transcription	Psoas Muscle	Psoas
39	chr15:99794200-99801000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr15:99794200-99802400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:99794200-99804000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr15:99794200-99804000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:99794200-99808600	Weak transcription	Pancreas	Pancrea
44	chr15:99794200-99814000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:99794200-99815600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:99794200-99815600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr15:99794200-99834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:99794200-99847000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr15:99794400-99799400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:99794400-99804000	Weak transcription	HMEC	breast

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