Variant report

Variant	rs6664
Chromosome Location	chr3:142841740-142841741
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:142841269-142842862	GM12878	blood:	n/a	n/a
2	FOXM1	chr3:142841226-142842765	GM12878	blood:	n/a	n/a
3	SPI1	chr3:142841520-142841776	K562	blood:	n/a	n/a
4	POLR2A	chr3:142837235-142842973	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:142841192-142842901	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:142837371-142841744	GM12892	blood:	n/a	n/a
7	POLR2A	chr3:142841306-142842861	GM12891	blood:	n/a	n/a
8	FOXM1	chr3:142841341-142842937	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:142837327-142842927	GM12891	blood:	n/a	n/a
10	REST	chr3:142841506-142841848	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:142836914-142843085	GM12891	blood:	n/a	n/a
12	POLR2A	chr3:142841273-142842915	GM12892	blood:	n/a	n/a
13	STAT3	chr3:142841428-142842095	GM12878	blood:	n/a	chr3:142841873-142841885
14	POLR2A	chr3:142837372-142842950	GM12891	blood:	n/a	n/a
15	POU2F2	chr3:142841370-142841758	GM12878	blood:	n/a	n/a
16	BCL11A	chr3:142841427-142841764	GM12878	blood:	n/a	n/a
17	SPI1	chr3:142841281-142842819	GM12878	blood:	n/a	chr3:142842634-142842643
18	ATF2	chr3:142841288-142842913	GM12878	blood:	n/a	n/a
19	SPI1	chr3:142841503-142841775	K562	blood:	n/a	n/a
20	STAT5A	chr3:142841159-142842913	GM12878	blood:	n/a	chr3:142841873-142841885
21	EGR1	chr3:142841505-142841761	K562	blood:	n/a	n/a
22	SP1	chr3:142841362-142841760	GM12878	blood:	n/a	n/a
23	POU2F2	chr3:142841579-142841749	GM12891	blood:	n/a	n/a
24	EP300	chr3:142841370-142842871	GM12878	blood:	n/a	chr3:142842629-142842643 chr3:142842630-142842639 chr3:142842657-142842671
25	PML	chr3:142841545-142841809	GM12878	blood:	n/a	n/a
26	RCOR1	chr3:142841392-142842926	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:142840725-142842754	GM12878	blood:	n/a	n/a
28	IRF4	chr3:142841383-142841801	GM12878	blood:	n/a	n/a
29	TBL1XR1	chr3:142841484-142842892	GM12878	blood:	n/a	n/a
30	SMC3	chr3:142841413-142842815	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:142841722-142841776	HUVEC	blood vessel:	n/a	n/a
32	NFIC	chr3:142841290-142842970	GM12878	blood:	n/a	n/a
33	CCNT2	chr3:142841525-142841834	K562	blood:	n/a	n/a
34	SP1	chr3:142841460-142841862	GM12878	blood:	n/a	n/a
35	EBF1	chr3:142841194-142841761	GM12878	blood:	n/a	n/a
36	EP300	chr3:142841520-142841866	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:142837654-142842994	GM12892	blood:	n/a	n/a
38	NFIC	chr3:142841264-142842915	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:142837455-142842924	GM18505	blood:	n/a	n/a
40	BCLAF1	chr3:142841375-142842934	GM12878	blood:	n/a	chr3:142842423-142842432 chr3:142842634-142842643
41	POLR2A	chr3:142841413-142842904	GM12892	blood:	n/a	n/a
42	JUND	chr3:142841599-142841767	K562	blood:	n/a	n/a
43	EP300	chr3:142841455-142841941	GM12878	blood:	n/a	n/a
44	NFATC1	chr3:142841375-142842905	GM12878	blood:	n/a	n/a
45	POLR2A	chr3:142841337-142842554	GM12891	blood:	n/a	n/a
46	SPI1	chr3:142841377-142841929	GM12891	blood:	n/a	n/a
47	SPI1	chr3:142841500-142841923	HL-60	blood:	n/a	n/a
48	POLR2A	chr3:142840091-142844969	K562	blood:	n/a	n/a
49	POLR2A	chr3:142841184-142843133	GM12878	blood:	n/a	n/a
50	TEAD4	chr3:142841190-142841825	K562	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:142841719-142841769	AG10803	skin:	n/a
2	chr3:142841719-142841769	Hepatocyte	liver:	n/a
3	chr3:142841719-142841769	MCF10A-Er-Src	breast:	n/a
4	chr3:142841719-142841769	HAEpiC	amniotic membrane:	n/a
5	chr3:142841719-142841769	SAEC	small airway:	n/a
6	chr3:142841719-142841769	LNCaP	prostate:	n/a
7	chr3:142841719-142841769	AG09319	gingival:	n/a
8	chr3:142841719-142841769	HUVEC	blood vessel:	n/a
9	chr3:142841719-142841769	SK-N-MC	brain:	n/a
10	chr3:142841719-142841769	HCM	heart:	n/a
11	chr3:142841719-142841769	GM19239	blood:	n/a
12	chr3:142841719-142841769	BE2_C	brain:	n/a
13	chr3:142841719-142841769	Caco-2	colon:	n/a
14	chr3:142841719-142841769	HL-60	blood:	n/a
15	chr3:142841719-142841769	CMK	blood:	n/a
16	chr3:142841719-142841769	HNPCEpiC	eye:	n/a
17	chr3:142841719-142841769	HEEpiC	esophagus:	n/a
18	chr3:142841719-142841769	AG04449	skin:	fetal
19	chr3:142841719-142841769	HCF	heart:	n/a
20	chr3:142841719-142841769	NH-A	brain:	n/a
21	chr3:142841719-142841769	H1-hESC	embryonic stem cell:	embryo
22	chr3:142841719-142841769	GM06990	blood:	n/a
23	chr3:142841719-142841769	PrEC	prostate:	n/a
24	chr3:142841719-142841769	MCF-7	breast:	n/a
25	chr3:142841719-142841769	HPAEpiC	pulmonary alveolar:	n/a
26	chr3:142841719-142841769	K562	blood:	n/a
27	chr3:142841719-142841769	AoSMC	blood vessel:	n/a
28	chr3:142841719-142841769	Hela-S3	cervix:	n/a
29	chr3:142841719-142841769	HMEC	breast:	n/a
30	chr3:142841719-142841769	U87	brain:	n/a
31	chr3:142841719-142841769	HCT-116	colon:	n/a
32	chr3:142841719-142841769	NHBE	bronchial:	n/a
33	chr3:142841719-142841769	AG09309	skin:	n/a
34	chr3:142841719-142841769	NHDF-neo	bronchial:	n/a
35	chr3:142841719-142841769	AG04450	lung:	fetal
36	chr3:142841719-142841769	RPTEC	kidney:	n/a
37	chr3:142841719-142841769	NT2-D1	testis:	n/a
38	chr3:142841719-142841769	SKMC	muscle:	n/a
39	chr3:142841719-142841769	ProgFib	skin:	n/a
40	chr3:142841719-142841769	PANC-1	pancreas:	n/a
41	chr3:142841719-142841769	GM12878	blood:	n/a
42	chr3:142841719-142841769	IMR90	lung:	fetal
43	chr3:142841719-142841769	PFSK-1	brain:	n/a
44	chr3:142841719-142841769	HepG2	liver:	n/a
45	chr3:142841719-142841769	T-47D	breast:	n/a
46	chr3:142841719-142841769	SK-N-SH	brain:	n/a
47	chr3:142841719-142841769	ECC-1	luminal epithelium:	n/a
48	chr3:142841719-142841769	A549	lung:	n/a
49	chr3:142841719-142841769	HRE	kidney:	n/a
50	chr3:142841719-142841769	Jurkat	blood:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:142841180..142845810-chr3:142884202..142887242,4	K562	blood:
2	chr3:142729466..142731298-chr3:142840071..142842956,2	K562	blood:
3	chr3:142839097..142841882-chr3:143060810..143062990,2	K562	blood:
4	chr3:142839696..142842108-chr3:143048440..143050143,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000241679	TF binding region
ENSG00000241679	CpG island
ENSG00000211483	Chromatin interaction
ENSG00000240012	Chromatin interaction
ENSG00000163714	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs11718140	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv2757893	chr3:142720230-142962932	Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759183	chr3:142720230-142964373	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS 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 target site	20 gene(s)	inside rSNPs	diseases
4	nsv591921	chr3:142762487-142841740	Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv949288	chr3:142793323-143585882	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1007164	chr3:142837004-142891719	Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv3421903	chr3:142839312-142842010	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6664	RASA2	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142837800-142843400	Active TSS	Fetal Kidney	kidney
2	chr3:142839200-142845800	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr3:142839200-142847200	Transcr. at gene 5' and 3'	Fetal Lung	lung
4	chr3:142839600-142843200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:142840000-142841800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:142840200-142842000	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:142840200-142842000	Transcr. at gene 5' and 3'	K562	blood
8	chr3:142840200-142842800	Weak transcription	Liver	Liver
9	chr3:142840200-142843000	Flanking Active TSS	GM12878-XiMat	blood
10	chr3:142840200-142843600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:142840400-142842200	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:142840400-142842200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
13	chr3:142840400-142842400	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr3:142840400-142843000	Enhancers	Primary hematopoietic stem cells	blood
15	chr3:142840400-142843400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:142840400-142843400	Weak transcription	HSMMtube	muscle
17	chr3:142840400-142843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:142840400-142843600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:142840600-142841800	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:142840600-142841800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:142840600-142842200	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr3:142840600-142842200	Weak transcription	NHLF	lung
23	chr3:142840600-142842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:142840600-142842400	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:142840600-142842600	Enhancers	Primary B cells from peripheral blood	blood
26	chr3:142840600-142842800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:142840600-142843200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:142840600-142843600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:142840600-142845200	Flanking Active TSS	Primary T cells from cord blood	blood
30	chr3:142840600-142854600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:142840800-142841800	Weak transcription	Brain Anterior Caudate	brain
32	chr3:142840800-142842200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:142840800-142843200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:142840800-142843600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr3:142840800-142843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:142840800-142843600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:142840800-142843800	Weak transcription	Pancreas	Pancrea
38	chr3:142841000-142842000	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:142841000-142842400	Weak transcription	Adipose Nuclei	Adipose
40	chr3:142841000-142842400	Weak transcription	Fetal Brain Female	brain
41	chr3:142841000-142842600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:142841000-142842800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:142841000-142843600	Weak transcription	HSMM	muscle
44	chr3:142841000-142843800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:142841000-142848600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:142841200-142841800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr3:142841200-142841800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr3:142841200-142841800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:142841200-142841800	Weak transcription	Esophagus	oesophagus
50	chr3:142841200-142841800	Active TSS	Thymus	Thymus

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