Variant report

Variant	rs37602
Chromosome Location	chr16:75505046-75505047
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr16:75505027-75505069	GM10266	blood:	n/a	n/a
2	CTCF	chr16:75505040-75505190	A549	lung:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75503918..75505841-chr16:75588439..75590620,2	MCF-7	breast:
2	chr16:75497399..75499829-chr16:75504719..75506935,2	K562	blood:
3	chr16:75503553..75505745-chr16:75588650..75591373,2	MCF-7	breast:
4	chr16:75498302..75501327-chr16:75504047..75506943,4	MCF-7	breast:
5	chr16:75503615..75506963-chr16:75549703..75552207,3	MCF-7	breast:
6	chr16:75503001..75505927-chr16:75587791..75590267,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000203472	TF binding region
ENSG00000262583	Chromatin interaction
ENSG00000166822	Chromatin interaction
ENSG00000261717	Chromatin interaction
ENSG00000205084	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1017239	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs1030262	0.80[ASN][1000 genomes]
rs10781977	0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10871308	0.81[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs10871313	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11149812	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs11149813	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs11149836	0.83[ASN][1000 genomes]
rs11641430	0.82[ASN][1000 genomes]
rs11643207	0.82[ASN][1000 genomes]
rs11645691	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs11646418	1.00[CEU][hapmap]
rs12445813	0.90[JPT][hapmap]
rs12918797	0.82[ASN][1000 genomes]
rs12928036	0.81[JPT][hapmap]
rs1424013	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1540	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17696831	0.82[ASN][1000 genomes]
rs1834013	0.82[ASN][1000 genomes]
rs1834014	0.82[ASN][1000 genomes]
rs185052	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs185053	0.93[ASN][1000 genomes]
rs1862705	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2059257	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs2242405	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs247423	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs247424	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs247425	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs247427	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs247431	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs247434	0.81[EUR][1000 genomes]
rs247436	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs247438	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs247443	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs247447	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs247450	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34539062	0.82[ASN][1000 genomes]
rs34918083	0.82[ASN][1000 genomes]
rs37588	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37589	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs37592	0.82[ASN][1000 genomes]
rs37593	0.82[ASN][1000 genomes]
rs37594	0.82[ASN][1000 genomes]
rs37595	0.82[ASN][1000 genomes]
rs37596	0.97[ASN][1000 genomes]
rs37599	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs37601	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs37605	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784936	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs3851735	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs40217	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40446	0.82[ASN][1000 genomes]
rs42472	1.00[CEU][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4536500	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs467780	0.82[EUR][1000 genomes]
rs468079	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4887827	0.88[ASN][1000 genomes]
rs4887828	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4887829	0.82[CHB][hapmap]
rs4887830	0.84[ASN][1000 genomes]
rs4888393	1.00[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4888396	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs4888430	0.85[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs4993971	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap]
rs62060550	0.82[ASN][1000 genomes]
rs62060551	0.82[ASN][1000 genomes]
rs62062595	0.85[EUR][1000 genomes]
rs6564261	0.83[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs7187690	0.93[CEU][hapmap]
rs7189407	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7195161	0.82[ASN][1000 genomes]
rs7201989	0.81[ASN][1000 genomes]
rs7202284	1.00[CEU][hapmap];0.91[JPT][hapmap]
rs766522	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs8046416	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs8048677	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs8048816	0.86[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs8050662	1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs8053632	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs8054586	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs8055490	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs8055609	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs8057084	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs889446	0.82[JPT][hapmap]
rs977985	0.81[ASN][1000 genomes]
rs977986	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs977987	0.83[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs9923834	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9928232	0.90[ASN][1000 genomes]
rs9934007	0.81[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer 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	64 gene(s)	inside rSNPs	diseases
5	esv2758432	chr16:75419614-75576971	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	esv2758657	chr16:75419614-75576971	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
10	esv3485939	chr16:75497453-75550284	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
11	esv3485940	chr16:75497453-75550284	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv572980	chr16:75505046-75549885	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs37602	TMEM170A	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75498600-75506800	Weak transcription	Brain Substantia Nigra	brain
2	chr16:75498600-75511800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr16:75498800-75505200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr16:75498800-75505600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr16:75498800-75505600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:75498800-75507200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:75498800-75518600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr16:75499000-75511000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr16:75499000-75511200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr16:75499000-75511200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr16:75499200-75505800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr16:75499200-75505800	Weak transcription	Fetal Heart	heart
13	chr16:75499200-75506000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr16:75499200-75506200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr16:75499200-75511400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr16:75499200-75511400	Weak transcription	Brain Anterior Caudate	brain
17	chr16:75499200-75519600	Weak transcription	Fetal Intestine Small	intestine
18	chr16:75499400-75505600	Weak transcription	Hela-S3	cervix
19	chr16:75501400-75506000	Weak transcription	HepG2	liver
20	chr16:75502400-75518200	Weak transcription	Aorta	Aorta
21	chr16:75504000-75506800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr16:75504400-75505400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr16:75505000-75505800	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr16:75505000-75507000	Enhancers	H1 Cell Line	embryonic stem cell

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