Variant report

Variant	rs561324234
Chromosome Location	chr3:120626526-120626527
allele	G/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	E2F6	chr3:120626471-120627765	H1-hESC	embryonic stem cell:	n/a	chr3:120626891-120626902 chr3:120626933-120626942 chr3:120627221-120627231 chr3:120626891-120626902 chr3:120627080-120627090 chr3:120626891-120626902
2	REST	chr3:120626072-120628339	H1-neurons	neurons:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627823-120627833 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
3	POLR2A	chr3:120626347-120627836	H1-neurons	neurons:	n/a	n/a
4	SP1	chr3:120626284-120627169	H1-hESC	embryonic stem cell:	n/a	chr3:120626800-120626812 chr3:120627026-120627038 chr3:120626932-120626941 chr3:120626932-120626946 chr3:120626803-120626824 chr3:120627026-120627038 chr3:120626973-120626982 chr3:120626931-120626943 chr3:120626932-120626942 chr3:120627023-120627037 chr3:120626931-120626943 chr3:120626932-120626942 chr3:120626800-120626811 chr3:120626932-120626941 chr3:120626933-120626942
5	RFX5	chr3:120626220-120627446	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr3:120626510-120627057	SK-N-SH	brain:	n/a	chr3:120626752-120626772 chr3:120626765-120626774
7	HA-E2F1	chr3:120626513-120627604	MCF-7	breast:	n/a	chr3:120626891-120626902 chr3:120626933-120626942 chr3:120627221-120627231 chr3:120626891-120626902 chr3:120627080-120627090 chr3:120626891-120626902
8	REST	chr3:120626461-120627584	A549	lung:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
9	REST	chr3:120626448-120627830	HL-60	blood:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
10	RAD21	chr3:120626513-120627627	H1-hESC	embryonic stem cell:	n/a	chr3:120627092-120627101
11	MAX	chr3:120626450-120626832	H1-hESC	embryonic stem cell:	n/a	chr3:120626801-120626811
12	CTBP2	chr3:120626470-120627895	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr3:120626524-120627234	H1-hESC	embryonic stem cell:	n/a	n/a
14	CREB1	chr3:120626466-120627458	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr3:120626257-120628925	SK-N-SH	brain:	n/a	n/a
16	MAX	chr3:120626498-120627826	H1-hESC	embryonic stem cell:	n/a	chr3:120626801-120626811
17	REST	chr3:120626475-120627638	H1-hESC	embryonic stem cell:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
18	SP1	chr3:120626368-120627271	H1-hESC	embryonic stem cell:	n/a	chr3:120626800-120626812 chr3:120627026-120627038 chr3:120626932-120626941 chr3:120626932-120626946 chr3:120626803-120626824 chr3:120627026-120627038 chr3:120626973-120626982 chr3:120626931-120626943 chr3:120626932-120626942 chr3:120627023-120627037 chr3:120626931-120626943 chr3:120626932-120626942 chr3:120626800-120626811 chr3:120626932-120626941 chr3:120626933-120626942
19	MAX	chr3:120626461-120627713	H1-hESC	embryonic stem cell:	n/a	chr3:120626801-120626811
20	POLR2A	chr3:120626526-120626785	H1-hESC	embryonic stem cell:	n/a	n/a
21	SP2	chr3:120626466-120627036	H1-hESC	embryonic stem cell:	n/a	chr3:120626751-120626774
22	POLR2A	chr3:120626384-120628307	H1-neurons	neurons:	n/a	n/a
23	REST	chr3:120626511-120627749	ECC-1	luminal epithelium:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
24	SP2	chr3:120626461-120626957	H1-hESC	embryonic stem cell:	n/a	chr3:120626751-120626774
25	SIN3A	chr3:120626338-120628654	H1-hESC	embryonic stem cell:	n/a	chr3:120627561-120627574 chr3:120627023-120627034 chr3:120627062-120627076 chr3:120627503-120627514 chr3:120627068-120627081
26	E2F6	chr3:120626439-120627417	H1-hESC	embryonic stem cell:	n/a	chr3:120626891-120626902 chr3:120626933-120626942 chr3:120627221-120627231 chr3:120626891-120626902 chr3:120627080-120627090 chr3:120626891-120626902
27	RFX5	chr3:120626524-120626994	H1-hESC	embryonic stem cell:	n/a	n/a
28	TBP	chr3:120626412-120627559	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr3:120626462-120627376	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr3:120626406-120627508	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
STXBP5L	TF binding region

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

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	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active 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 miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv3431805	chr3:120626112-120628860	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120626000-120627800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr3:120626200-120626600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr3:120626200-120626600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:120626200-120628000	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:120626200-120628000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr3:120626200-120628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr3:120626200-120628800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr3:120626200-120629000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr3:120626200-120630200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr3:120626400-120626600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:120626400-120626600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:120626400-120626600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:120626400-120626600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
14	chr3:120626400-120626600	Enhancers	Brain Hippocampus Middle	brain
15	chr3:120626400-120626600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:120626400-120626600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
17	chr3:120626400-120626600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
18	chr3:120626400-120626600	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
19	chr3:120626400-120626800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:120626400-120626800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:120626400-120626800	Enhancers	Pancreas	Pancrea
22	chr3:120626400-120627200	Active TSS	Fetal Brain Female	brain
23	chr3:120626400-120627800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:120626400-120627800	Active TSS	Fetal Brain Male	brain
25	chr3:120626400-120627800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
26	chr3:120626400-120628000	Bivalent/Poised TSS	Brain Germinal Matrix	brain
27	chr3:120626400-120628000	Active TSS	Fetal Kidney	kidney
28	chr3:120626400-120628400	Active TSS	Brain Cingulate Gyrus	brain
29	chr3:120626400-120628400	Active TSS	Rectal Smooth Muscle	rectum
30	chr3:120626400-120628600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:120626400-120628600	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr3:120626400-120628600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:120626400-120628600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr3:120626400-120628600	Active TSS	Brain Anterior Caudate	brain
35	chr3:120626400-120628800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:120626400-120628800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr3:120626400-120628800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:120626400-120629200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:120626400-120630400	Active TSS	Brain Angular Gyrus	brain
40	chr3:120626400-120630400	Active TSS	Brain Inferior Temporal Lobe	brain

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