Variant report

Variant	rs4965490
Chromosome Location	chr15:99981269-99981270
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99979583..99981872-chr15:99983556..99985309,2	MCF-7	breast:
2	chr15:99974033..99977897-chr15:99978912..99982934,5	K562	blood:
3	chr15:99979674..99981771-chr15:99994725..99997256,2	K562	blood:
4	chr15:99977572..99979807-chr15:99980072..99982815,2	K562	blood:
5	chr15:99981264..99984715-chr15:99985641..99987973,4	MCF-7	breast:
6	chr15:99981180..99982961-chr15:99993073..99995315,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11247094	0.81[ASN][1000 genomes]
rs12050818	0.81[ASN][1000 genomes]
rs12903392	0.81[ASN][1000 genomes]
rs12909582	0.81[ASN][1000 genomes]
rs1545246	0.92[CHD][hapmap];0.88[JPT][hapmap]
rs1561864	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs1561866	0.81[ASN][1000 genomes]
rs1561868	0.92[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2119939	0.83[ASN][1000 genomes]
rs28393358	0.81[ASN][1000 genomes]
rs28463528	0.81[ASN][1000 genomes]
rs2862151	0.81[ASN][1000 genomes]
rs4965234	0.87[JPT][hapmap]
rs4965235	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4965489	0.81[ASN][1000 genomes]
rs4965493	0.91[CHB][hapmap];0.96[CHD][hapmap];0.80[GIH][hapmap]
rs6598247	0.81[ASN][1000 genomes]
rs6598248	0.81[ASN][1000 genomes]
rs6598249	0.91[CHB][hapmap]
rs7162570	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162817	0.90[ASN][1000 genomes]
rs7165066	0.90[ASN][1000 genomes]
rs7167464	0.88[CHD][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7169461	0.88[JPT][hapmap]
rs7169660	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs7170529	0.90[ASN][1000 genomes]
rs7182313	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs8028527	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
11	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv904549	chr15:99940221-99991506	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv519800	chr15:99950772-99987109	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv904552	chr15:99954278-99982447	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv904553	chr15:99954278-99983175	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv904555	chr15:99956954-99981269	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv904556	chr15:99956954-99987109	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv904557	chr15:99956954-99991506	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	nsv519319	chr15:99972661-99991506	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
20	nsv570728	chr15:99973369-99986764	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4965490	TTC23	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99974200-99982000	Weak transcription	Gastric	stomach
2	chr15:99974200-99984000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr15:99974400-99982000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:99975000-99982200	Enhancers	Fetal Heart	heart
5	chr15:99976000-99982000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr15:99976000-99982000	Weak transcription	Pancreas	Pancrea
7	chr15:99976000-99982200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr15:99976000-99982200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr15:99976200-99981400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:99976400-99981600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:99976400-99981600	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:99976400-99981600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:99976400-99982000	Weak transcription	HSMM	muscle
14	chr15:99976600-99981400	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:99976600-99982000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr15:99976600-99984800	Enhancers	Fetal Muscle Leg	muscle
17	chr15:99976800-99981400	Weak transcription	Hela-S3	cervix
18	chr15:99976800-99982400	Weak transcription	Brain Hippocampus Middle	brain
19	chr15:99978000-99981400	Weak transcription	Colonic Mucosa	Colon
20	chr15:99978000-99981400	Weak transcription	Spleen	Spleen
21	chr15:99978200-99981600	Weak transcription	Stomach Mucosa	stomach
22	chr15:99978400-99982000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr15:99978400-99982000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr15:99978400-99982200	Weak transcription	Primary B cells from cord blood	blood
25	chr15:99978600-99981400	Weak transcription	NHLF	lung
26	chr15:99978800-99981400	Weak transcription	HSMMtube	muscle
27	chr15:99978800-99982000	Weak transcription	Fetal Intestine Small	intestine
28	chr15:99978800-99982200	Weak transcription	Psoas Muscle	Psoas
29	chr15:99978800-99983000	Weak transcription	Aorta	Aorta
30	chr15:99979000-99982200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr15:99979000-99982200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:99979200-99981400	Weak transcription	Fetal Lung	lung
33	chr15:99979200-99982000	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:99979200-99982000	Weak transcription	Ovary	ovary
35	chr15:99979200-99982200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:99979200-99982200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:99979200-99995800	Enhancers	Fetal Thymus	thymus
38	chr15:99979400-99981600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:99979400-99982000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr15:99979400-99982000	Weak transcription	HUVEC	blood vessel
41	chr15:99979400-99982200	Weak transcription	Dnd41	blood
42	chr15:99979400-99984000	Weak transcription	Brain Anterior Caudate	brain
43	chr15:99979400-99987000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:99979400-99987400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr15:99979600-99981400	Weak transcription	Fetal Kidney	kidney
46	chr15:99979600-99982000	Weak transcription	NH-A	brain
47	chr15:99979600-99983200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:99979800-99981600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:99980200-99982000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:99980400-99981600	Enhancers	NHDF-Ad	bronchial

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