Variant report

Variant	rs71324984
Chromosome Location	chr3:49709147-49709148
allele	A/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	POLR2A	chr3:49709102-49709422	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr3:49708911-49709654	HCT-116	colon:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
3	CTCF	chr3:49709114-49709470	GM19240	blood:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
4	CTCF	chr3:49709135-49709478	GM19238	blood:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
5	NRF1	chr3:49709074-49709449	H1-hESC	embryonic stem cell:	n/a	n/a
6	BHLHE40	chr3:49708684-49709339	HepG2	liver:	n/a	n/a
7	MAZ	chr3:49709105-49709424	HepG2	liver:	n/a	n/a
8	TEAD4	chr3:49709091-49709482	K562	blood:	n/a	n/a
9	POLR2A	chr3:49708940-49709502	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr3:49709031-49709477	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr3:49709070-49709436	Hela-S3	cervix:	n/a	n/a
12	MXI1	chr3:49708760-49709424	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49709036-49709452	Hela-S3	cervix:	n/a	n/a
14	MYBL2	chr3:49708516-49709516	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:49709121-49709322	ProgFib	skin:	n/a	n/a
16	CTCF	chr3:49709043-49709483	A549	lung:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
17	RAD21	chr3:49709051-49709454	HepG2	liver:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
18	RAD21	chr3:49709120-49709582	ECC-1	luminal epithelium:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
19	RAD21	chr3:49709041-49709516	SK-N-SH_RA	brain:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
20	CTCF	chr3:49709147-49709462	MCF-7	breast:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
21	CTCF	chr3:49709131-49709498	K562	blood:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
22	SMC3	chr3:49709071-49709509	GM12878	blood:	n/a	chr3:49709310-49709320 chr3:49709310-49709324
23	YY1	chr3:49709097-49709430	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr3:49708920-49709878	A549	lung:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
25	POLR2A	chr3:49708694-49709339	HepG2	liver:	n/a	n/a
26	NFIC	chr3:49708536-49709444	HepG2	liver:	n/a	n/a
27	RAD21	chr3:49708721-49709784	HCT-116	colon:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
28	RAD21	chr3:49708837-49709514	HepG2	liver:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
29	RAD21	chr3:49709085-49709538	IMR90	lung:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
30	POLR2A	chr3:49709096-49709279	MCF-7	breast:	n/a	n/a
31	RAD21	chr3:49708852-49709713	SK-N-SH	brain:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
32	CTCF	chr3:49709135-49709436	SK-N-SH_RA	brain:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
33	POU2F2	chr3:49708982-49709468	GM12891	blood:	n/a	n/a
34	HCFC1	chr3:49709069-49709638	Hela-S3	cervix:	n/a	n/a
35	POLR2A	chr3:49707209-49709609	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:49709127-49709423	H1-hESC	embryonic stem cell:	n/a	n/a
37	RAD21	chr3:49709130-49709511	SK-N-SH_RA	brain:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
38	ARID3A	chr3:49708776-49709391	HepG2	liver:	n/a	n/a
39	NFATC1	chr3:49709009-49709527	GM12878	blood:	n/a	n/a
40	RAD21	chr3:49709001-49709478	MCF-7	breast:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
41	CTCF	chr3:49708228-49709922	SK-N-SH	brain:	n/a	chr3:49709311-49709321 chr3:49709308-49709326 chr3:49709310-49709323 chr3:49709303-49709324 chr3:49709314-49709323
42	RAD21	chr3:49708898-49709604	H1-hESC	embryonic stem cell:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
43	POLR2A	chr3:49709040-49709510	PANC-1	pancreas:	n/a	n/a
44	NFIC	chr3:49708601-49709210	HepG2	liver:	n/a	n/a
45	MAFF	chr3:49708778-49709340	HepG2	liver:	n/a	n/a
46	MBD4	chr3:49708516-49709412	HepG2	liver:	n/a	n/a
47	YY1	chr3:49709107-49709441	GM12878	blood:	n/a	n/a
48	RAD21	chr3:49709109-49709440	K562	blood:	n/a	chr3:49709306-49709325 chr3:49709308-49709320 chr3:49709309-49709322 chr3:49709310-49709320
49	SMC3	chr3:49708617-49709781	SK-N-SH	brain:	n/a	chr3:49709310-49709320 chr3:49709310-49709324
50	SMC3	chr3:49709127-49709489	K562	blood:	n/a	chr3:49709310-49709320 chr3:49709310-49709324

No.	Distal block	Cell Line	Cell type
1	chr3:49576858..49578074-chr3:49708760..49709826,8	K562	blood:
2	chr3:49573379..49575748-chr3:49707460..49709611,2	MCF-7	breast:
3	chr3:49575867..49578786-chr3:49708422..49711347,4	K562	blood:
4	chr3:49577156..49579797-chr3:49709101..49710779,3	K562	blood:
5	chr3:49609338..49612017-chr3:49707292..49709835,2	K562	blood:
6	chr3:49603620..49605380-chr3:49707989..49710873,2	MCF-7	breast:
7	chr3:49576811..49578018-chr3:49708915..49709864,14	MCF-7	breast:
8	chr3:49576201..49578760-chr3:49706386..49709294,3	MCF-7	breast:
9	chr3:49600383..49601196-chr3:49708840..49709817,2	MCF-7	breast:
10	chr3:49507427..49510910-chr3:49706254..49709319,3	MCF-7	breast:
11	chr3:49709088..49712884-chr3:49714614..49717582,5	MCF-7	breast:
12	chr3:49576717..49578036-chr3:49708771..49709800,6	MCF-7	breast:
13	chr3:49708866..49715375-chr3:49724746..49730407,6	K562	blood:

Variant related genes	Relation type
APEH	TF binding region
ENSG00000173531	Chromatin interaction
ENSG00000164068	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13061156	0.81[AMR][1000 genomes]
rs13071087	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13100791	0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3206653	0.81[AMR][1000 genomes]
rs35620248	0.81[AMR][1000 genomes]
rs36116071	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49686600-49710600	Weak transcription	Right Atrium	heart
2	chr3:49690400-49710600	Weak transcription	Brain Substantia Nigra	brain
3	chr3:49692200-49710400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:49695200-49710600	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr3:49700000-49710600	Weak transcription	Fetal Brain Male	brain
6	chr3:49702400-49710600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49703400-49709400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:49703600-49710600	Weak transcription	Left Ventricle	heart
9	chr3:49703600-49710600	Weak transcription	Right Ventricle	heart
10	chr3:49703600-49710600	Weak transcription	Spleen	Spleen
11	chr3:49703800-49710600	Enhancers	Liver	Liver
12	chr3:49703800-49710600	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:49704200-49710600	Weak transcription	Gastric	stomach
14	chr3:49704400-49710600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:49704600-49709400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:49704600-49710600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:49704600-49710600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr3:49704800-49710600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr3:49705000-49710600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:49705600-49710600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:49705600-49710600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:49705600-49710600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:49706000-49710600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:49706200-49710600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:49706200-49710600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:49706200-49710600	Weak transcription	Fetal Intestine Large	intestine
27	chr3:49706200-49710600	Weak transcription	Fetal Intestine Small	intestine
28	chr3:49706800-49709600	Weak transcription	Fetal Kidney	kidney
29	chr3:49706800-49710600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:49706800-49710600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:49706800-49710600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49706800-49710600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:49706800-49710600	Weak transcription	Stomach Mucosa	stomach
34	chr3:49707000-49709400	Weak transcription	Hela-S3	cervix
35	chr3:49707000-49710600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:49707000-49710600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:49707000-49710600	Weak transcription	Adipose Nuclei	Adipose
38	chr3:49707000-49710600	Weak transcription	Esophagus	oesophagus
39	chr3:49707000-49710600	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:49707000-49710600	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr3:49707000-49710600	Weak transcription	HSMM	muscle
42	chr3:49707000-49710600	Weak transcription	NH-A	brain
43	chr3:49707000-49710600	Weak transcription	NHEK	skin
44	chr3:49707000-49710600	Weak transcription	Osteobl	bone
45	chr3:49707200-49710600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:49707200-49710600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:49707200-49710600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:49707200-49710600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr3:49707200-49710600	Weak transcription	HSMMtube	muscle
50	chr3:49707400-49710600	Weak transcription	Fetal Muscle Trunk	muscle

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