Variant report

Variant	rs71386939
Chromosome Location	chr16:71928693-71928694
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	TAF1	chr16:71928538-71929822	MCF-7	breast:	n/a	n/a
2	TCF12	chr16:71927822-71930235	A549	lung:	n/a	n/a
3	PBX3	chr16:71928682-71929804	A549	lung:	n/a	n/a
4	POLR2A	chr16:71928104-71930257	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr16:71927836-71930365	MCF-7	breast:	n/a	n/a
6	MYBL2	chr16:71927838-71930298	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:71928653-71929736	SK-N-SH	brain:	n/a	n/a
8	MAX	chr16:71928692-71930193	MCF-7	breast:	n/a	n/a
9	POLR2A	chr16:71928214-71930152	GM18951	blood:	n/a	n/a
10	CEBPD	chr16:71928632-71929786	HepG2	liver:	n/a	n/a
11	CHD2	chr16:71928626-71930214	GM12878	blood:	n/a	chr16:71929163-71929173
12	NR2F2	chr16:71928677-71930404	MCF-7	breast:	n/a	chr16:71930156-71930171
13	POLR2A	chr16:71928189-71930271	GM12878	blood:	n/a	n/a
14	HEY1	chr16:71928615-71929789	HepG2	liver:	n/a	n/a
15	GABPA	chr16:71928030-71930358	MCF-7	breast:	n/a	chr16:71929165-71929174 chr16:71929394-71929403
16	SIN3AK20	chr16:71928618-71929848	PANC-1	pancreas:	n/a	n/a
17	MBD4	chr16:71928538-71929715	HepG2	liver:	n/a	n/a
18	RELA	chr16:71928222-71929678	GM15510	blood:	n/a	n/a
19	POLR2A	chr16:71927839-71930117	HepG2	liver:	n/a	n/a
20	TCF12	chr16:71928692-71929561	HepG2	liver:	n/a	n/a
21	POLR2A	chr16:71928153-71930279	PBDE	blood:	n/a	n/a
22	POLR2A	chr16:71928194-71930157	GM18505	blood:	n/a	n/a
23	GATA3	chr16:71928623-71930187	A549	lung:	n/a	chr16:71929206-71929215 chr16:71929203-71929210
24	MTA3	chr16:71928065-71930392	GM12878	blood:	n/a	n/a
25	MYC	chr16:71928130-71930212	K562	blood:	n/a	n/a
26	CTBP2	chr16:71928544-71929817	H1-hESC	embryonic stem cell:	n/a	n/a
27	EP300	chr16:71928693-71929533	HepG2	liver:	n/a	n/a
28	YY1	chr16:71928515-71928782	GM12891	blood:	n/a	n/a
29	POLR2A	chr16:71928624-71930182	SK-N-MC	brain:	n/a	n/a
30	TBL1XR1	chr16:71928668-71929830	GM12878	blood:	n/a	n/a
31	POLR2A	chr16:71928291-71929945	MCF-7	breast:	n/a	n/a
32	POLR2A	chr16:71928015-71930265	H1-hESC	embryonic stem cell:	n/a	n/a
33	STAT5A	chr16:71928474-71930023	GM12878	blood:	n/a	n/a
34	HDAC2	chr16:71928640-71929695	HepG2	liver:	n/a	chr16:71929009-71929017
35	POLR2A	chr16:71927984-71930237	GM12878	blood:	n/a	n/a
36	POLR2A	chr16:71928132-71930180	GM19099	blood:	n/a	n/a
37	UBTF	chr16:71928111-71930288	K562	blood:	n/a	n/a
38	NR2F2	chr16:71928331-71930344	K562	blood:	n/a	chr16:71930156-71930171
39	CREB1	chr16:71928206-71929794	GM12878	blood:	n/a	n/a
40	PML	chr16:71928079-71929860	GM12878	blood:	n/a	n/a
41	MTA3	chr16:71928654-71929093	GM12878	blood:	n/a	n/a
42	TEAD4	chr16:71928079-71929698	K562	blood:	n/a	n/a
43	SIN3AK20	chr16:71928569-71930264	MCF-7	breast:	n/a	n/a
44	HNF4A	chr16:71928608-71929612	HepG2	liver:	n/a	chr16:71929010-71929018 chr16:71929009-71929017 chr16:71928873-71928888 chr16:71928874-71928887 chr16:71929003-71929018 chr16:71929003-71929018 chr16:71929003-71929018 chr16:71928872-71928887 chr16:71928874-71928886 chr16:71928873-71928887 chr16:71928874-71928886 chr16:71928871-71928889 chr16:71928999-71929021
45	SMARCB1	chr16:71927948-71930213	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr16:71927940-71930138	HepG2	liver:	n/a	n/a
47	POLR2A	chr16:71928608-71929697	HepG2	liver:	n/a	n/a
48	MAX	chr16:71928618-71930344	A549	lung:	n/a	n/a
49	HDAC2	chr16:71928630-71929840	HepG2	liver:	n/a	chr16:71929009-71929017
50	REST	chr16:71927961-71930362	H1-neurons	neurons:	n/a	chr16:71928812-71928832 chr16:71930143-71930157 chr16:71930145-71930155 chr16:71928818-71928832 chr16:71930205-71930215

No.	Distal block	Cell Line	Cell type
1	chr16:71927209..71930992-chr16:71962077..71965660,4	K562	blood:
2	chr16:71913385..71915141-chr16:71927812..71929318,2	MCF-7	breast:
3	chr16:71841145..71844669-chr16:71927071..71931411,13	MCF-7	breast:
4	chr16:71927384..71929645-chr16:71963039..71965792,3	MCF-7	breast:
5	chr16:71928455..71931068-chr16:71956099..71958859,3	MCF-7	breast:
6	chr16:71756273..71758753-chr16:71927656..71930818,3	MCF-7	breast:
7	chr16:71755635..71758602-chr16:71927230..71929480,2	MCF-7	breast:
8	chr16:71927209..71930992-chr16:71962077..71965220,3	K562	blood:
9	chr16:71923118..71926504-chr16:71927692..71930407,4	K562	blood:
10	chr16:71927590..71930855-chr16:71952254..71956665,4	MCF-7	breast:
11	chr16:71840867..71844185-chr16:71927744..71931104,8	K562	blood:
12	chr16:71916766..71921844-chr16:71926616..71932994,12	K562	blood:
13	chr16:71916483..71919796-chr16:71926616..71929598,5	K562	blood:
14	chr16:71928144..71931559-chr16:72041567..72044276,4	MCF-7	breast:
15	chr16:71841370..71844789-chr16:71927787..71931052,12	MCF-7	breast:
16	chr16:71927973..71929865-chr16:72045946..72047910,3	MCF-7	breast:
17	chr16:71927888..71929610-chr16:72042486..72044051,2	MCF-7	breast:
18	chr16:71927023..71929738-chr16:72042635..72044988,2	K562	blood:

Variant related genes	Relation type
IST1	TF binding region
ENSG00000102967	Chromatin interaction
ENSG00000263320	Chromatin interaction
ENSG00000040199	Chromatin interaction
ENSG00000166747	Chromatin interaction
ENSG00000261513	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000182149	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10500567	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10852507	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11075906	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11639843	0.89[ASN][1000 genomes]
rs11640135	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11644740	0.89[ASN][1000 genomes]
rs11865456	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12149307	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12149325	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12149917	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445564	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12445641	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12448086	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12921279	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921459	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12927691	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12934512	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13330178	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17357420	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17358402	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28667298	0.82[ASN][1000 genomes]
rs2878494	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3088285	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34029919	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34101687	0.89[ASN][1000 genomes]
rs34664834	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35028754	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35209006	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35404791	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35535529	0.95[EUR][1000 genomes]
rs35595148	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36182990	0.89[ASN][1000 genomes]
rs3751820	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4528577	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71384781	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71384782	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386940	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71386942	0.89[ASN][1000 genomes]
rs7185027	0.89[EUR][1000 genomes]
rs7188591	0.91[EUR][1000 genomes]
rs7191848	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7195988	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7197486	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7198834	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7200447	0.82[ASN][1000 genomes]
rs73586164	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8046044	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8049508	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8050058	0.93[ASN][1000 genomes]
rs8052358	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8053906	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8063657	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9940234	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71927600-71928800	Active TSS	Fetal Brain Female	brain
2	chr16:71927600-71930400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr16:71927600-71930800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr16:71927800-71928800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
5	chr16:71927800-71928800	Active TSS	Brain Germinal Matrix	brain
6	chr16:71927800-71929000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr16:71927800-71929400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:71927800-71929800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr16:71927800-71930400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr16:71927800-71930400	Active TSS	Brain Anterior Caudate	brain
11	chr16:71927800-71930400	Active TSS	Osteobl	bone
12	chr16:71927800-71930600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr16:71927800-71930600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr16:71927800-71930600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr16:71927800-71930600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr16:71927800-71930600	Active TSS	Fetal Kidney	kidney
17	chr16:71927800-71930600	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr16:71927800-71930600	Active TSS	Rectal Smooth Muscle	rectum
19	chr16:71927800-71930800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr16:71927800-71930800	Active TSS	NHLF	lung
21	chr16:71927800-71931000	Active TSS	H9 Cell Line	embryonic stem cell
22	chr16:71927800-71931000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr16:71927800-71931200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr16:71927800-71931200	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr16:71927800-71931200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr16:71927800-71931200	Active TSS	Right Ventricle	heart
27	chr16:71927800-71931200	Active TSS	HSMM	muscle
28	chr16:71927800-71931400	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr16:71927800-71931400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr16:71928000-71928800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr16:71928000-71928800	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr16:71928000-71929000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr16:71928000-71929000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr16:71928000-71929000	Active TSS	Right Atrium	heart
35	chr16:71928000-71929400	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr16:71928000-71929600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:71928000-71930200	Active TSS	Pancreas	Pancrea
38	chr16:71928000-71930400	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr16:71928000-71930400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr16:71928000-71930400	Active TSS	Primary T killer memory cells from peripheral blood	blood
41	chr16:71928000-71930400	Active TSS	Brain Angular Gyrus	brain
42	chr16:71928000-71930400	Active TSS	Brain Substantia Nigra	brain
43	chr16:71928000-71930400	Active TSS	Fetal Stomach	stomach
44	chr16:71928000-71930400	Active TSS	NHEK	skin
45	chr16:71928000-71930600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr16:71928000-71930600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr16:71928000-71930600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr16:71928000-71930600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr16:71928000-71930600	Active TSS	Brain Cingulate Gyrus	brain
50	chr16:71928000-71930600	Active TSS	Brain Hippocampus Middle	brain

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