Variant report

Variant	rs34391207
Chromosome Location	chr3:23958481-23958482
allele	A/G
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	RAD21	chr3:23958095-23958753	H1-hESC	embryonic stem cell:	n/a	chr3:23958465-23958475
2	SIX5	chr3:23958263-23958879	GM12878	blood:	n/a	chr3:23958533-23958547 chr3:23958537-23958546 chr3:23958535-23958544
3	POLR2A	chr3:23958138-23959197	A549	lung:	n/a	n/a
4	EP300	chr3:23958064-23959381	A549	lung:	n/a	n/a
5	REST	chr3:23958374-23958896	PFSK-1	brain:	n/a	chr3:23958595-23958608
6	RUNX3	chr3:23957822-23959408	GM12878	blood:	n/a	n/a
7	ATF2	chr3:23958232-23959402	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFIC	chr3:23958296-23958936	HepG2	liver:	n/a	n/a
9	ETS1	chr3:23957956-23959417	K562	blood:	n/a	chr3:23958534-23958547 chr3:23958533-23958546 chr3:23958596-23958607
10	CTCF	chr3:23958438-23958583	NHEK	skin:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
11	RELA	chr3:23958138-23959259	GM15510	blood:	n/a	n/a
12	CTCF	chr3:23958410-23958675	GM12892	blood:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
13	CTCF	chr3:23958380-23958530	HA-sp	spinal cord:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
14	CTCF	chr3:23958407-23958651	Fibrobl	skin:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
15	ELF1	chr3:23958363-23958896	HepG2	liver:	n/a	n/a
16	HEY1	chr3:23958136-23959699	HepG2	liver:	n/a	chr3:23958483-23958498
17	CTCF	chr3:23958380-23958530	GM12869	blood:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
18	POLR2A	chr3:23958105-23960665	K562	blood:	n/a	n/a
19	YY1	chr3:23958063-23959381	K562	blood:	n/a	chr3:23958483-23958494 chr3:23958485-23958494 chr3:23958491-23958505
20	NR2F2	chr3:23958128-23958918	K562	blood:	n/a	n/a
21	POLR2A	chr3:23957987-23959405	K562	blood:	n/a	n/a
22	ELK1	chr3:23958050-23959249	K562	blood:	n/a	n/a
23	CTCF	chr3:23958380-23958530	GM12871	blood:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
24	TCF3	chr3:23958268-23958924	GM12878	blood:	n/a	n/a
25	GTF2F1	chr3:23958020-23959283	Hela-S3	cervix:	n/a	n/a
26	YY1	chr3:23958448-23959331	GM12892	blood:	n/a	chr3:23958483-23958494 chr3:23958485-23958494 chr3:23958491-23958505
27	SIX5	chr3:23958037-23959387	A549	lung:	n/a	chr3:23958533-23958547 chr3:23958537-23958546 chr3:23958535-23958544
28	JUND	chr3:23958469-23959248	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr3:23958098-23960725	GM12878	blood:	n/a	n/a
30	USF1	chr3:23958370-23958695	SK-N-SH_RA	brain:	n/a	n/a
31	POLR2A	chr3:23958121-23960749	SK-N-SH	brain:	n/a	n/a
32	MEF2A	chr3:23958302-23958937	GM12878	blood:	n/a	n/a
33	CTCF	chr3:23958416-23958622	Pancreas_OC	pancreas:	n/a	chr3:23958512-23958525 chr3:23958464-23958474 chr3:23958515-23958524 chr3:23958462-23958475
34	EP300	chr3:23958302-23959238	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:23958042-23960224	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr3:23958118-23960215	GM12891	blood:	n/a	n/a
37	TAF1	chr3:23958269-23959240	GM12878	blood:	n/a	n/a
38	CREB1	chr3:23957957-23959395	HepG2	liver:	n/a	n/a
39	GABPA	chr3:23958016-23959458	MCF-7	breast:	n/a	n/a
40	TCF12	chr3:23958360-23958856	GM12878	blood:	n/a	n/a
41	POLR2A	chr3:23957960-23959774	GM12878	blood:	n/a	n/a
42	RAD21	chr3:23957951-23958667	H1-hESC	embryonic stem cell:	n/a	chr3:23958465-23958475 chr3:23958030-23958044
43	SIN3AK20	chr3:23958349-23958763	PFSK-1	brain:	n/a	n/a
44	CEBPB	chr3:23958317-23959420	K562	blood:	n/a	n/a
45	SMC3	chr3:23957820-23958909	Hela-S3	cervix:	n/a	chr3:23958465-23958475 chr3:23958514-23958521
46	POLR2A	chr3:23958170-23960433	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr3:23958360-23958510	HCM	heart:	n/a	chr3:23958464-23958474 chr3:23958462-23958475
48	POLR2A	chr3:23958032-23960247	GM12891	blood:	n/a	n/a
49	POLR2A	chr3:23958128-23960836	K562	blood:	n/a	n/a
50	CHD1	chr3:23957214-23960192	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:23956507..23958836-chr3:25705831..25708315,2	K562	blood:
2	chr12:76425682..76426603-chr3:23958326..23959064,2	HCT-116	colon:
3	chr3:23846380..23850116-chr3:23956700..23960461,6	MCF-7	breast:
4	chr3:23850301..23853237-chr3:23957517..23960615,4	MCF-7	breast:
5	chr3:23958135..23959121-chrX:47003925..47004575,2	NB4	blood:
6	chr15:42787482..42788209-chr3:23958299..23959137,2	Hela-S3	cervix:
7	chr17:58167241..58170093-chr3:23957521..23960210,2	MCF-7	breast:
8	chr22:29998884..29999633-chr3:23958298..23958926,2	NB4	blood:
9	chr3:23958025..23958690-chrX:77166038..77167009,2	Hela-S3	cervix:
10	chr3:23957476..23960072-chr3:25467685..25470119,2	K562	blood:
11	chr2:96068327..96068925-chr3:23957909..23958508,2	Hela-S3	cervix:
12	chr3:23958447..23959124-chr7:139025718..139026246,2	Hela-S3	cervix:
13	chr3:23956080..23959048-chr3:23995915..23997492,2	MCF-7	breast:
14	chr1:203059673..203062550-chr3:23957552..23960185,2	MCF-7	breast:
15	chr12:96336327..96336872-chr3:23958243..23958926,2	NB4	blood:
16	chr3:23852479..23855481-chr3:23956917..23960502,4	MCF-7	breast:
17	chr3:23954505..23971330-chr3:23977357..23992645,61	MCF-7	breast:
18	chr19:19496705..19497560-chr3:23958156..23958868,2	NB4	blood:
19	chr16:1661843..1662391-chr3:23958190..23959085,2	Hela-S3	cervix:
20	chr3:23957534..23959919-chr3:25823926..25825755,2	K562	blood:
21	chr3:23848988..23853074-chr3:23957156..23960234,5	K562	blood:
22	chr3:23845112..23848622-chr3:23958029..23961906,4	K562	blood:
23	chr3:23956631..23966740-chr3:23975650..23993173,64	MCF-7	breast:
24	chr3:23957572..23960051-chr3:23995970..23999234,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPL15-1	chr3:23958276-23958571	NONHSAT088690

Variant related genes	Relation type
RPL15	TF binding region
NKIRAS1	TF binding region
ENSG00000165972	Chromatin interaction
ENSG00000257839	Chromatin interaction
ENSG00000182872	Chromatin interaction
ENSG00000186575	Chromatin interaction
ENSG00000187535	Chromatin interaction
ENSG00000269955	Chromatin interaction
ENSG00000115042	Chromatin interaction
ENSG00000261040	Chromatin interaction
ENSG00000163485	Chromatin interaction
ENSG00000223791	Chromatin interaction
ENSG00000077097	Chromatin interaction
ENSG00000165240	Chromatin interaction
ENSG00000197885	Chromatin interaction
ENSG00000264219	Chromatin interaction
ENSG00000092531	Chromatin interaction
ENSG00000077092	Chromatin interaction
ENSG00000170142	Chromatin interaction
ENSG00000007545	Chromatin interaction
ENSG00000151093	Chromatin interaction
ENSG00000248503	Chromatin interaction
ENSG00000151092	Chromatin interaction
ENSG00000164898	Chromatin interaction
ENSG00000174738	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000147123	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs34200392	1.00[AFR][1000 genomes]
rs34927065	0.81[AFR][1000 genomes]
rs34993633	1.00[AFR][1000 genomes]
rs35569243	1.00[AFR][1000 genomes]
rs35752010	0.81[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 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	chr3:23956800-23959200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:23956800-23959400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:23956800-23959400	Active TSS	Brain Angular Gyrus	brain
4	chr3:23957000-23959400	Active TSS	Colon Smooth Muscle	Colon
5	chr3:23957000-23959600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr3:23957000-23959600	Active TSS	H9 Cell Line	embryonic stem cell
7	chr3:23957000-23959600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:23957000-23960400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:23957000-23960600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:23957000-23960600	Active TSS	Right Atrium	heart
11	chr3:23957200-23959400	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr3:23957200-23959600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:23957200-23959600	Active TSS	Stomach Smooth Muscle	stomach
14	chr3:23957200-23959600	Active TSS	HSMMtube	muscle
15	chr3:23957200-23960200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:23957200-23960800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:23957400-23958800	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:23957400-23959000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:23957400-23959200	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr3:23957400-23959400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:23957400-23959400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:23957400-23959400	Active TSS	HSMM	muscle
23	chr3:23957400-23959600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:23957400-23959600	Active TSS	Brain Anterior Caudate	brain
25	chr3:23957400-23959600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr3:23957400-23959600	Active TSS	Fetal Stomach	stomach
27	chr3:23957400-23959600	Active TSS	Left Ventricle	heart
28	chr3:23957400-23959600	Active TSS	Rectal Smooth Muscle	rectum
29	chr3:23957400-23959600	Active TSS	GM12878-XiMat	blood
30	chr3:23957400-23959600	Active TSS	NHDF-Ad	bronchial
31	chr3:23957400-23959800	Active TSS	Ovary	ovary
32	chr3:23957400-23960800	Active TSS	Psoas Muscle	Psoas
33	chr3:23957400-23960800	Active TSS	Right Ventricle	heart
34	chr3:23957600-23958600	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:23957600-23958800	Active TSS	Muscle Satellite Cultured Cells	--
36	chr3:23957600-23958800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:23957600-23958800	Active TSS	Brain Germinal Matrix	brain
38	chr3:23957600-23959200	Active TSS	NHEK	skin
39	chr3:23957600-23959400	Active TSS	H1 Cell Line	embryonic stem cell
40	chr3:23957600-23959400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:23957600-23959400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:23957600-23959400	Active TSS	Brain Substantia Nigra	brain
43	chr3:23957600-23959400	Active TSS	Fetal Brain Female	brain
44	chr3:23957600-23959400	Active TSS	Fetal Lung	lung
45	chr3:23957600-23959400	Active TSS	NHLF	lung
46	chr3:23957600-23959600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr3:23957600-23959600	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr3:23957600-23959600	Active TSS	Liver	Liver
49	chr3:23957600-23959600	Active TSS	Brain Hippocampus Middle	brain
50	chr3:23957600-23959600	Active TSS	Fetal Brain Male	brain

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