Variant report

Variant	rs13332180
Chromosome Location	chr16:71929859-71929860
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr16:71927822-71930235	A549	lung:	n/a	n/a
2	ELF1	chr16:71928804-71930284	GM12878	blood:	n/a	chr16:71929326-71929335 chr16:71929820-71929832 chr16:71929527-71929538
3	POLR2A	chr16:71928104-71930257	GM12878	blood:	n/a	n/a
4	SIN3AK20	chr16:71927836-71930365	MCF-7	breast:	n/a	n/a
5	NR2F2	chr16:71928967-71930301	K562	blood:	n/a	chr16:71930156-71930171
6	TAF1	chr16:71928778-71930216	H1-neurons	neurons:	n/a	n/a
7	MYBL2	chr16:71927838-71930298	HepG2	liver:	n/a	n/a
8	TAF1	chr16:71928701-71930236	ECC-1	luminal epithelium:	n/a	n/a
9	MAX	chr16:71928692-71930193	MCF-7	breast:	n/a	n/a
10	MYC	chr16:71928975-71929859	MCF-7	breast:	n/a	n/a
11	POLR2A	chr16:71928214-71930152	GM18951	blood:	n/a	n/a
12	CHD2	chr16:71928626-71930214	GM12878	blood:	n/a	chr16:71929163-71929173
13	NR2F2	chr16:71928677-71930404	MCF-7	breast:	n/a	chr16:71930156-71930171
14	POLR2A	chr16:71928189-71930271	GM12878	blood:	n/a	n/a
15	GABPA	chr16:71928030-71930358	MCF-7	breast:	n/a	chr16:71929165-71929174 chr16:71929394-71929403
16	TAF1	chr16:71928818-71930120	MCF-7	breast:	n/a	n/a
17	TBL1XR1	chr16:71928940-71930017	K562	blood:	n/a	n/a
18	MAX	chr16:71928749-71930218	ECC-1	luminal epithelium:	n/a	n/a
19	POLR2A	chr16:71929825-71930242	GM12891	blood:	n/a	n/a
20	GABPA	chr16:71928720-71930034	K562	blood:	n/a	chr16:71929165-71929174 chr16:71929394-71929403
21	POLR2A	chr16:71928737-71929935	PFSK-1	brain:	n/a	n/a
22	ELF1	chr16:71928858-71930305	GM12878	blood:	n/a	chr16:71929326-71929335 chr16:71929820-71929832 chr16:71929527-71929538
23	TFAP2C	chr16:71928812-71930136	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr16:71927839-71930117	HepG2	liver:	n/a	n/a
25	UBTF	chr16:71928727-71930298	K562	blood:	n/a	n/a
26	YY1	chr16:71928873-71930235	SK-N-SH_RA	brain:	n/a	chr16:71929427-71929443 chr16:71929428-71929438 chr16:71929270-71929284 chr16:71929818-71929832 chr16:71929428-71929450 chr16:71929818-71929827 chr16:71929426-71929443 chr16:71929264-71929275 chr16:71929431-71929439
27	POLR2A	chr16:71928745-71930240	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr16:71928153-71930279	PBDE	blood:	n/a	n/a
29	TAF1	chr16:71928698-71929986	HepG2	liver:	n/a	n/a
30	POLR2A	chr16:71928194-71930157	GM18505	blood:	n/a	n/a
31	MYC	chr16:71928927-71930197	NB4	blood:	n/a	n/a
32	YY1	chr16:71928842-71930159	K562	blood:	n/a	chr16:71929427-71929443 chr16:71929428-71929438 chr16:71929270-71929284 chr16:71929818-71929832 chr16:71929428-71929450 chr16:71929818-71929827 chr16:71929426-71929443 chr16:71929264-71929275 chr16:71929431-71929439
33	ETS1	chr16:71928862-71930186	K562	blood:	n/a	chr16:71929394-71929405
34	GATA3	chr16:71928623-71930187	A549	lung:	n/a	chr16:71929206-71929215 chr16:71929203-71929210
35	MTA3	chr16:71928065-71930392	GM12878	blood:	n/a	n/a
36	MYC	chr16:71928130-71930212	K562	blood:	n/a	n/a
37	CHD2	chr16:71928757-71930262	Hela-S3	cervix:	n/a	chr16:71929163-71929173
38	POLR2A	chr16:71928624-71930182	SK-N-MC	brain:	n/a	n/a
39	SIN3AK20	chr16:71929005-71929911	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr16:71928291-71929945	MCF-7	breast:	n/a	n/a
41	WRNIP1	chr16:71928968-71930267	GM12878	blood:	n/a	n/a
42	POLR2A	chr16:71928015-71930265	H1-hESC	embryonic stem cell:	n/a	n/a
43	HMGN3	chr16:71928900-71929985	K562	blood:	n/a	n/a
44	YY1	chr16:71928921-71930244	GM12878	blood:	n/a	chr16:71929427-71929443 chr16:71929428-71929438 chr16:71929270-71929284 chr16:71929818-71929832 chr16:71929428-71929450 chr16:71929818-71929827 chr16:71929426-71929443 chr16:71929264-71929275 chr16:71929431-71929439
45	STAT5A	chr16:71928474-71930023	GM12878	blood:	n/a	n/a
46	POLR2A	chr16:71928784-71930193	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr16:71928766-71929962	HUVEC	blood vessel:	n/a	n/a
48	POLR2A	chr16:71927984-71930237	GM12878	blood:	n/a	n/a
49	POLR2A	chr16:71928132-71930180	GM19099	blood:	n/a	n/a
50	UBTF	chr16:71928111-71930288	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr16:71927209..71930992-chr16:71962077..71965660,4	K562	blood:
2	chr16:71841145..71844669-chr16:71927071..71931411,13	MCF-7	breast:
3	chr1:150601356..150602327-chr16:71929417..71930053,2	Hela-S3	cervix:
4	chr16:71929421..71930061-chrX:23925311..23926168,2	Hela-S3	cervix:
5	chr16:71928455..71931068-chr16:71956099..71958859,3	MCF-7	breast:
6	chr16:71756273..71758753-chr16:71927656..71930818,3	MCF-7	breast:
7	chr11:71791494..71792387-chr16:71929263..71929932,2	Hela-S3	cervix:
8	chr16:71927209..71930992-chr16:71962077..71965220,3	K562	blood:
9	chr16:71923118..71926504-chr16:71927692..71930407,4	K562	blood:
10	chr16:71929075..71929880-chr8:144679540..144680239,2	Hela-S3	cervix:
11	chr16:71878320..71880402-chr16:71929242..71933378,4	MCF-7	breast:
12	chr16:71927590..71930855-chr16:71952254..71956665,4	MCF-7	breast:
13	chr16:71840867..71844185-chr16:71927744..71931104,8	K562	blood:
14	chr16:71916766..71921844-chr16:71926616..71932994,12	K562	blood:
15	chr16:71928144..71931559-chr16:72041567..72044276,4	MCF-7	breast:
16	chr16:71841370..71844789-chr16:71927787..71931052,12	MCF-7	breast:
17	chr16:71927973..71929865-chr16:72045946..72047910,3	MCF-7	breast:
18	chr16:71929035..71931345-chr16:71958752..71961424,2	K562	blood:
19	chr16:71842406..71843188-chr16:71928972..71929897,2	MCF-7	breast:
20	chr16:71929403..71929942-chr9:132251291..132251975,2	Hela-S3	cervix:

Variant related genes	Relation type
ZNF821	TF binding region
ENSG00000261337	Chromatin interaction
ENSG00000137497	Chromatin interaction
ENSG00000182149	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000179886	Chromatin interaction
ENSG00000165182	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000184831	Chromatin interaction
ENSG00000040199	Chromatin interaction
ENSG00000104529	Chromatin interaction
ENSG00000261513	Chromatin interaction
ENSG00000102967	Chromatin interaction
ENSG00000263320	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000204054	Chromatin interaction
ENSG00000224470	Chromatin interaction
ENSG00000143420	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1035543	0.91[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs11075910	0.82[ASW][hapmap]
rs11539980	0.81[ASW][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs12051425	0.92[GIH][hapmap]
rs12447856	0.88[MEX][hapmap];0.91[TSI][hapmap]
rs12598902	0.83[YRI][hapmap]
rs12600153	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12600163	1.00[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12925901	0.85[JPT][hapmap]
rs12930206	0.80[MEX][hapmap];0.91[TSI][hapmap]
rs13332113	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13337118	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1392487	0.81[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs17286411	0.85[JPT][hapmap]
rs1834033	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2036338	0.84[MEX][hapmap];0.91[TSI][hapmap]
rs2270830	0.80[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs2270831	0.87[ASW][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap]
rs2278031	0.87[ASW][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2291947	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2303220	0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[MKK][hapmap]
rs34111614	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4538017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4788448	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788551	0.81[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs4788558	0.80[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs4788567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4788568	0.82[ASW][hapmap]
rs4788572	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788574	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4788578	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4788587	0.92[GIH][hapmap]
rs55702379	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56309616	0.88[EUR][1000 genomes]
rs60075093	0.88[EUR][1000 genomes]
rs60740701	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7204798	0.92[GIH][hapmap]
rs7350856	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8058762	0.81[ASN][1000 genomes]
rs918721	0.81[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs952159	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs952160	0.94[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9889100	0.83[EUR][1000 genomes]
rs9921270	0.81[ASW][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs9925228	0.81[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]
rs9925441	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9925684	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9929683	0.83[YRI][hapmap]
rs9932707	0.82[ASW][hapmap]
rs9936965	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9937626	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9939455	0.81[ASW][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13332180	TMEM208	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71927600-71930400	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr16:71927600-71930800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr16:71927800-71930400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr16:71927800-71930400	Active TSS	Brain Anterior Caudate	brain
5	chr16:71927800-71930400	Active TSS	Osteobl	bone
6	chr16:71927800-71930600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr16:71927800-71930600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr16:71927800-71930600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr16:71927800-71930600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr16:71927800-71930600	Active TSS	Fetal Kidney	kidney
11	chr16:71927800-71930600	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr16:71927800-71930600	Active TSS	Rectal Smooth Muscle	rectum
13	chr16:71927800-71930800	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr16:71927800-71930800	Active TSS	NHLF	lung
15	chr16:71927800-71931000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr16:71927800-71931000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr16:71927800-71931200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr16:71927800-71931200	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr16:71927800-71931200	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr16:71927800-71931200	Active TSS	Right Ventricle	heart
21	chr16:71927800-71931200	Active TSS	HSMM	muscle
22	chr16:71927800-71931400	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr16:71927800-71931400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr16:71928000-71930200	Active TSS	Pancreas	Pancrea
25	chr16:71928000-71930400	Active TSS	Primary T helper naive cells from peripheral blood	blood
26	chr16:71928000-71930400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr16:71928000-71930400	Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr16:71928000-71930400	Active TSS	Brain Angular Gyrus	brain
29	chr16:71928000-71930400	Active TSS	Brain Substantia Nigra	brain
30	chr16:71928000-71930400	Active TSS	Fetal Stomach	stomach
31	chr16:71928000-71930400	Active TSS	NHEK	skin
32	chr16:71928000-71930600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr16:71928000-71930600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr16:71928000-71930600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr16:71928000-71930600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr16:71928000-71930600	Active TSS	Brain Cingulate Gyrus	brain
37	chr16:71928000-71930600	Active TSS	Brain Hippocampus Middle	brain
38	chr16:71928000-71930600	Active TSS	Colonic Mucosa	Colon
39	chr16:71928000-71930600	Active TSS	Colon Smooth Muscle	Colon
40	chr16:71928000-71930600	Active TSS	Fetal Heart	heart
41	chr16:71928000-71930600	Active TSS	Fetal Lung	lung
42	chr16:71928000-71930600	Active TSS	Small Intestine	intestine
43	chr16:71928000-71930600	Bivalent/Poised TSS	HepG2	liver
44	chr16:71928000-71930600	Active TSS	NHDF-Ad	bronchial
45	chr16:71928000-71930800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr16:71928000-71930800	Active TSS	Stomach Mucosa	stomach
47	chr16:71928000-71931000	Active TSS	Left Ventricle	heart
48	chr16:71928000-71931000	Active TSS	Psoas Muscle	Psoas
49	chr16:71928000-71931000	Active TSS	A549	lung
50	chr16:71928000-71931200	Active TSS	H1 Cell Line	embryonic stem cell

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