Variant report

Variant	rs3796639
Chromosome Location	chr4:20702103-20702104
allele	A/C
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	chr4:20701588-20702450	K562	blood:	n/a	n/a
2	POLR2A	chr4:20701771-20702219	A549	lung:	n/a	n/a
3	POLR2A	chr4:20701646-20702437	MCF-7	breast:	n/a	n/a
4	TCF12	chr4:20701616-20702396	ECC-1	luminal epithelium:	n/a	n/a
5	CTCF	chr4:20701960-20702110	AG04449	skin:	n/a	n/a
6	MXI1	chr4:20701627-20702474	HepG2	liver:	n/a	chr4:20701956-20701971 chr4:20701886-20701895 chr4:20701954-20701969
7	POLR2A	chr4:20701615-20702322	HCT-116	colon:	n/a	n/a
8	POLR2A	chr4:20701610-20702729	GM12878	blood:	n/a	n/a
9	TBP	chr4:20701547-20702420	K562	blood:	n/a	n/a
10	POLR2A	chr4:20701737-20702239	A549	lung:	n/a	n/a
11	MXI1	chr4:20701308-20702550	GM12878	blood:	n/a	chr4:20701956-20701971 chr4:20701886-20701895 chr4:20701954-20701969
12	CHD2	chr4:20701763-20702164	HepG2	liver:	n/a	n/a
13	MYC	chr4:20701664-20702206	HepG2	liver:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
14	MAFK	chr4:20701546-20702316	K562	blood:	n/a	n/a
15	JUND	chr4:20701666-20702311	H1-hESC	embryonic stem cell:	n/a	chr4:20702028-20702037
16	POLR2A	chr4:20701612-20702375	SK-N-SH	brain:	n/a	n/a
17	USF1	chr4:20701694-20702129	K562	blood:	n/a	n/a
18	POLR2A	chr4:20701624-20702363	K562	blood:	n/a	n/a
19	CTCF	chr4:20702000-20702150	SAEC	small airway:	n/a	n/a
20	POLR2A	chr4:20701700-20702319	GM12878	blood:	n/a	n/a
21	POLR2A	chr4:20701727-20702279	A549	lung:	n/a	n/a
22	MYC	chr4:20701115-20702209	MCF10A-Er-Src	breast:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
23	RCOR1	chr4:20701766-20702554	K562	blood:	n/a	n/a
24	MYC	chr4:20701667-20702214	MCF-7	breast:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
25	POLR2A	chr4:20701557-20702370	HepG2	liver:	n/a	n/a
26	YY1	chr4:20701781-20702239	K562	blood:	n/a	n/a
27	FOS	chr4:20701949-20702143	MCF10A-Er-Src	breast:	n/a	chr4:20702028-20702037
28	RUNX3	chr4:20701734-20702289	GM12878	blood:	n/a	n/a
29	MAX	chr4:20701578-20702189	K562	blood:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
30	EBF1	chr4:20701795-20702189	GM12878	blood:	n/a	n/a
31	STAT3	chr4:20701949-20702302	MCF10A-Er-Src	breast:	n/a	n/a
32	TAF1	chr4:20701536-20702339	H1-neurons	neurons:	n/a	n/a
33	SIN3AK20	chr4:20701762-20702219	PFSK-1	brain:	n/a	n/a
34	POLR2A	chr4:20701718-20702298	GM10847	blood:	n/a	n/a
35	MAX	chr4:20701645-20702205	HepG2	liver:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
36	POLR2A	chr4:20701677-20702351	A549	lung:	n/a	n/a
37	MAX	chr4:20701543-20702390	HepG2	liver:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
38	NFYB	chr4:20701705-20702383	K562	blood:	n/a	n/a
39	POLR2A	chr4:20701463-20702494	U87	brain:	n/a	n/a
40	HDAC2	chr4:20701700-20702340	H1-hESC	embryonic stem cell:	n/a	n/a
41	TAF1	chr4:20701668-20702284	GM12878	blood:	n/a	n/a
42	MAX	chr4:20701476-20702295	SK-N-SH	brain:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701884-20701895 chr4:20701885-20701895
43	SIN3AK20	chr4:20701659-20702452	H1-hESC	embryonic stem cell:	n/a	n/a
44	MAZ	chr4:20701237-20702281	HepG2	liver:	n/a	chr4:20701885-20701894 chr4:20701885-20701895 chr4:20701881-20701896 chr4:20701886-20701893 chr4:20701884-20701895 chr4:20701885-20701894 chr4:20701884-20701895 chr4:20701885-20701895
45	TBL1XR1	chr4:20701649-20702296	GM12878	blood:	n/a	n/a
46	USF2	chr4:20701722-20702169	H1-hESC	embryonic stem cell:	n/a	chr4:20701884-20701895
47	ATF3	chr4:20701701-20702121	K562	blood:	n/a	chr4:20702026-20702037 chr4:20702029-20702039 chr4:20702028-20702039 chr4:20702026-20702039 chr4:20702028-20702048 chr4:20702025-20702040 chr4:20702029-20702037 chr4:20702029-20702036
48	TBL1XR1	chr4:20701838-20702299	K562	blood:	n/a	n/a
49	POLR2A	chr4:20701643-20702243	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr4:20701679-20702353	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:20701536..20702331-chr9:91933301..91933855,2	Hela-S3	cervix:
2	chr4:20700245..20702604-chr4:20707211..20709448,2	MCF-7	breast:
3	chr4:20700439..20703043-chr4:20709421..20711457,2	MCF-7	breast:
4	chr4:20693086..20698959-chr4:20699230..20704175,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLIT2-2	chr4:20702061-20702329	NONHSAT095736

Variant related genes	Relation type
PACRGL	TF binding region
ENSG00000187742	Chromatin interaction
ENSG00000163138	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10017693	1.00[ASN][1000 genomes]
rs10018931	0.87[ASN][1000 genomes]
rs10022322	0.97[ASN][1000 genomes]
rs10024002	1.00[ASN][1000 genomes]
rs10025286	1.00[ASN][1000 genomes]
rs10034054	0.87[ASN][1000 genomes]
rs10938801	0.89[ASN][1000 genomes]
rs11941041	0.98[ASN][1000 genomes]
rs11944886	0.87[ASN][1000 genomes]
rs12331966	0.87[ASN][1000 genomes]
rs12641186	0.89[ASN][1000 genomes]
rs12644782	0.84[ASN][1000 genomes]
rs16869851	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16869886	0.87[ASN][1000 genomes]
rs16869889	1.00[ASN][1000 genomes]
rs1985322	0.84[ASN][1000 genomes]
rs2052775	0.97[ASN][1000 genomes]
rs2114472	0.87[ASN][1000 genomes]
rs2114473	0.84[ASN][1000 genomes]
rs2288308	0.97[ASN][1000 genomes]
rs28524474	1.00[ASN][1000 genomes]
rs28637181	0.83[ASN][1000 genomes]
rs28714128	0.94[ASN][1000 genomes]
rs28788006	1.00[ASN][1000 genomes]
rs3764964	0.87[ASN][1000 genomes]
rs3764965	0.87[ASN][1000 genomes]
rs3764966	0.87[ASN][1000 genomes]
rs3764967	1.00[ASN][1000 genomes]
rs3815872	1.00[ASN][1000 genomes]
rs4510461	1.00[ASN][1000 genomes]
rs55794413	0.89[ASN][1000 genomes]
rs55874299	0.89[ASN][1000 genomes]
rs56152829	0.89[ASN][1000 genomes]
rs57740160	0.94[ASN][1000 genomes]
rs59335491	1.00[ASN][1000 genomes]
rs62410092	0.80[ASN][1000 genomes]
rs62410099	0.89[ASN][1000 genomes]
rs62410126	1.00[ASN][1000 genomes]
rs62410129	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62410159	0.97[ASN][1000 genomes]
rs62411662	0.92[ASN][1000 genomes]
rs6447974	0.97[ASN][1000 genomes]
rs6447976	0.84[ASN][1000 genomes]
rs6811030	0.84[ASN][1000 genomes]
rs6811505	0.84[ASN][1000 genomes]
rs6815738	0.87[ASN][1000 genomes]
rs6817475	0.82[ASN][1000 genomes]
rs73240292	1.00[ASN][1000 genomes]
rs7438098	0.94[ASN][1000 genomes]
rs755155	0.80[ASN][1000 genomes]
rs7655154	0.97[ASN][1000 genomes]
rs7666288	1.00[ASN][1000 genomes]
rs7673805	0.84[ASN][1000 genomes]
rs7674453	1.00[ASN][1000 genomes]
rs7681691	0.87[ASN][1000 genomes]
rs7696618	1.00[ASN][1000 genomes]
rs990206	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013077	chr4:20599841-20732558	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1010145	chr4:20601908-21057992	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv537052	chr4:20601908-21057992	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1014941	chr4:20611726-21345226	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv537053	chr4:20611726-21345226	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv829876	chr4:20638736-20835621	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:20701000-20702400	Active TSS	Brain Anterior Caudate	brain
2	chr4:20701000-20702800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr4:20701000-20703200	Active TSS	Skeletal Muscle Female	skeletal muscle
4	chr4:20701000-20703400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:20701200-20702400	Active TSS	Brain Cingulate Gyrus	brain
6	chr4:20701200-20702400	Active TSS	Fetal Heart	heart
7	chr4:20701200-20702600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:20701200-20702600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:20701200-20702600	Active TSS	Brain Substantia Nigra	brain
10	chr4:20701200-20702800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr4:20701200-20702800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:20701200-20702800	Active TSS	Fetal Muscle Trunk	muscle
13	chr4:20701200-20702800	Active TSS	Rectal Smooth Muscle	rectum
14	chr4:20701200-20702800	Active TSS	Right Atrium	heart
15	chr4:20701200-20703000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr4:20701200-20703000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:20701200-20703000	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr4:20701200-20703000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr4:20701200-20703000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr4:20701200-20703000	Active TSS	Fetal Kidney	kidney
21	chr4:20701200-20703200	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr4:20701200-20703200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr4:20701200-20703200	Active TSS	Right Ventricle	heart
24	chr4:20701200-20703400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr4:20701400-20702400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:20701400-20702400	Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr4:20701400-20702400	Active TSS	Primary T helper cells PMA-I stimulated	--
28	chr4:20701400-20702400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
29	chr4:20701400-20702400	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr4:20701400-20702400	Active TSS	Fetal Stomach	stomach
31	chr4:20701400-20702400	Active TSS	Thymus	Thymus
32	chr4:20701400-20702600	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr4:20701400-20702600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:20701400-20702600	Active TSS	Brain Angular Gyrus	brain
35	chr4:20701400-20702600	Active TSS	Brain Germinal Matrix	brain
36	chr4:20701400-20702600	Active TSS	Brain Hippocampus Middle	brain
37	chr4:20701400-20702600	Active TSS	Colon Smooth Muscle	Colon
38	chr4:20701400-20702600	Active TSS	Fetal Brain Male	brain
39	chr4:20701400-20702600	Active TSS	Fetal Intestine Large	intestine
40	chr4:20701400-20702600	Active TSS	Fetal Lung	lung
41	chr4:20701400-20702600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:20701400-20702800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:20701400-20702800	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr4:20701400-20702800	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr4:20701400-20702800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr4:20701400-20702800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr4:20701400-20702800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:20701400-20702800	Active TSS	Aorta	Aorta
49	chr4:20701400-20702800	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr4:20701400-20702800	Active TSS	Fetal Intestine Small	intestine

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