Variant report

Variant	rs6761463
Chromosome Location	chr2:50201547-50201548
allele	C/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	GABPA	chr2:50201180-50201629	A549	lung:	n/a	n/a
2	NRF1	chr2:50200942-50201617	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:50201020-50201618	U87	brain:	n/a	n/a
4	NFYB	chr2:50201158-50201554	GM12878	blood:	n/a	n/a
5	PBX3	chr2:50201006-50201621	SK-N-SH	brain:	n/a	chr2:50201346-50201355
6	POLR2A	chr2:50201107-50201635	U87	brain:	n/a	n/a
7	MAX	chr2:50201154-50201560	H1-hESC	embryonic stem cell:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
8	MAX	chr2:50201047-50201596	SK-N-SH	brain:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
9	USF1	chr2:50201042-50201611	SK-N-SH_RA	brain:	n/a	chr2:50201350-50201361
10	USF1	chr2:50201120-50201565	A549	lung:	n/a	chr2:50201350-50201361
11	GABPA	chr2:50201148-50201629	A549	lung:	n/a	n/a
12	USF1	chr2:50201107-50201581	H1-hESC	embryonic stem cell:	n/a	chr2:50201350-50201361
13	POLR2A	chr2:50201082-50201653	SK-N-MC	brain:	n/a	n/a
14	REST	chr2:50199676-50201874	H1-neurons	neurons:	n/a	chr2:50200054-50200067
15	FOXP2	chr2:50201193-50201591	SK-N-MC	brain:	n/a	n/a
16	USF1	chr2:50201092-50201558	A549	lung:	n/a	chr2:50201350-50201361
17	GATA3	chr2:50200994-50201673	SK-N-SH	brain:	n/a	chr2:50201391-50201401
18	SETDB1	chr2:50201066-50201638	U2OS	brain:	n/a	n/a
19	POLR2A	chr2:50200659-50201665	H1-neurons	neurons:	n/a	n/a
20	GATA3	chr2:50200950-50201598	SH-SY5Y	brain:	n/a	chr2:50201391-50201401
21	FOXA2	chr2:50201291-50201557	A549	lung:	n/a	n/a
22	MAX	chr2:50201124-50201646	A549	lung:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
23	POLR2A	chr2:50200642-50201618	H1-neurons	neurons:	n/a	n/a
24	USF1	chr2:50200960-50201633	H1-hESC	embryonic stem cell:	n/a	chr2:50201350-50201361
25	USF2	chr2:50201162-50201549	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:50201145-50201680	SK-N-MC	brain:	n/a	n/a
27	PBX3	chr2:50200974-50201639	SK-N-SH	brain:	n/a	chr2:50201346-50201355
28	POLR2A	chr2:50201026-50201612	U87	brain:	n/a	n/a
29	POLR2A	chr2:50201195-50201668	SK-N-SH	brain:	n/a	n/a
30	POLR2A	chr2:50201066-50201635	U87	brain:	n/a	n/a
31	MXI1	chr2:50199140-50201817	SK-N-SH	brain:	n/a	n/a
32	MAX	chr2:50201044-50201660	A549	lung:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
33	USF1	chr2:50201038-50201605	SK-N-SH	brain:	n/a	chr2:50201350-50201361
34	GATA2	chr2:50200922-50201708	SH-SY5Y	brain:	n/a	chr2:50201391-50201401
35	POLR2A	chr2:50201434-50201585	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:50201269-50201566	H1-hESC	embryonic stem cell:	n/a	n/a
37	USF1	chr2:50201042-50201630	SK-N-SH	brain:	n/a	chr2:50201350-50201361
38	E2F6	chr2:50201245-50201581	A549	lung:	n/a	n/a
39	GATA3	chr2:50200893-50201619	SK-N-SH	brain:	n/a	chr2:50201391-50201401
40	MAX	chr2:50201110-50201635	SK-N-SH	brain:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
41	E2F6	chr2:50201129-50201637	A549	lung:	n/a	chr2:50201592-50201601

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:50201511-50201561	NHBE	bronchial:	n/a
2	chr2:50201511-50201561	HCT-116	colon:	n/a
3	chr2:50201505-50201555	A549	lung:	n/a
4	chr2:50201505-50201555	GM19239	blood:	n/a
5	chr2:50201505-50201555	MCF-7	breast:	n/a
6	chr2:50201505-50201555	AG04449	skin:	fetal
7	chr2:50201511-50201561	NT2-D1	testis:	n/a
8	chr2:50201511-50201561	Hepatocyte	liver:	n/a
9	chr2:50201511-50201561	PrEC	prostate:	n/a
10	chr2:50201511-50201561	HRCEpiC	kidney:	n/a
11	chr2:50201511-50201561	ProgFib	skin:	n/a
12	chr2:50201505-50201555	Hela-S3	cervix:	n/a
13	chr2:50201511-50201561	NHDF-neo	bronchial:	n/a
14	chr2:50201511-50201561	AoSMC	blood vessel:	n/a
15	chr2:50201511-50201561	HNPCEpiC	eye:	n/a
16	chr2:50201511-50201561	PANC-1	pancreas:	n/a
17	chr2:50201511-50201561	RPTEC	kidney:	n/a
18	chr2:50201511-50201561	Caco-2	colon:	n/a
19	chr2:50201505-50201555	HEEpiC	esophagus:	n/a
20	chr2:50201511-50201561	K562	blood:	n/a
21	chr2:50201511-50201561	BJ	skin:	n/a
22	chr2:50201505-50201555	SAEC	small airway:	n/a
23	chr2:50201505-50201555	IMR90	lung:	fetal
24	chr2:50201505-50201555	HRPEpiC	eye:	n/a
25	chr2:50201511-50201561	PFSK-1	brain:	n/a
26	chr2:50201505-50201555	Hepatocyte	liver:	n/a
27	chr2:50201511-50201561	NH-A	brain:	n/a
28	chr2:50201505-50201555	HCPEpiC	choroid plexus:	n/a
29	chr2:50201511-50201561	H1-hESC	embryonic stem cell:	embryo
30	chr2:50201505-50201555	NHDF-neo	bronchial:	n/a
31	chr2:50201511-50201561	HCF	heart:	n/a
32	chr2:50201505-50201555	PFSK-1	brain:	n/a
33	chr2:50201505-50201555	MCF10A-Er-Src	breast:	n/a
34	chr2:50201511-50201561	SK-N-MC	brain:	n/a
35	chr2:50201505-50201555	CMK	blood:	n/a
36	chr2:50201511-50201561	A549	lung:	n/a
37	chr2:50201505-50201555	HMEC	breast:	n/a
38	chr2:50201511-50201561	NB4	blood:	n/a
39	chr2:50201511-50201561	AG04449	skin:	fetal
40	chr2:50201505-50201555	HCF	heart:	n/a
41	chr2:50201511-50201561	AG04450	lung:	fetal
42	chr2:50201511-50201561	SAEC	small airway:	n/a
43	chr2:50201511-50201561	HepG2	liver:	n/a
44	chr2:50201505-50201555	AG10803	skin:	n/a
45	chr2:50201505-50201555	HL-60	blood:	n/a
46	chr2:50201505-50201555	H1-hESC	embryonic stem cell:	embryo
47	chr2:50201511-50201561	Hela-S3	cervix:	n/a
48	chr2:50201505-50201555	GM12891	blood:	n/a
49	chr2:50201511-50201561	T-47D	breast:	n/a
50	chr2:50201505-50201555	PrEC	prostate:	n/a

Variant related genes	Relation type
NRXN1	TF binding region
NRXN1	CpG island

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs12470829	0.92[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12478797	0.93[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1363036	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1363052	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1369295	0.93[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1369297	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1421567	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs1421569	0.93[CHB][hapmap]
rs1421577	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1421598	0.93[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes]
rs1469002	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1469003	0.93[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1477248	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs1477249	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1541642	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1592728	0.83[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs1865490	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2193865	0.92[EUR][1000 genomes]
rs2351149	0.91[CEU][hapmap];0.89[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2859977	0.93[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4583505	0.82[CHB][hapmap];0.83[EUR][1000 genomes]
rs4971632	0.93[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4971635	0.82[JPT][hapmap]
rs6545137	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6545144	0.86[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6706484	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706613	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6712956	0.85[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs6714990	0.93[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7562931	0.83[EUR][1000 genomes]
rs7596020	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs930295	0.93[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9636391	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs980794	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[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	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932839	chr2:50181785-50225697	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50198800-50201800	Active TSS	Brain Angular Gyrus	brain
2	chr2:50199600-50201600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:50199600-50201800	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr2:50199800-50201800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr2:50199800-50201800	Active TSS	Brain Anterior Caudate	brain
6	chr2:50199800-50201800	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:50200000-50201800	Active TSS	Fetal Brain Female	brain
8	chr2:50200600-50201800	Active TSS	Brain Germinal Matrix	brain
9	chr2:50200600-50201800	Active TSS	Fetal Kidney	kidney
10	chr2:50200800-50201800	Active TSS	Brain Hippocampus Middle	brain
11	chr2:50200800-50201800	Active TSS	Fetal Intestine Small	intestine
12	chr2:50200800-50201800	Active TSS	Right Atrium	heart
13	chr2:50200800-50205600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:50201000-50201600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr2:50201000-50201600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr2:50201000-50201600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr2:50201000-50201600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr2:50201000-50201600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr2:50201000-50201600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr2:50201000-50201600	Active TSS	Primary B cells from cord blood	blood
21	chr2:50201000-50201600	Active TSS	Primary T cells fromperipheralblood	blood
22	chr2:50201000-50201600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr2:50201000-50201600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr2:50201000-50201600	Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr2:50201000-50201600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:50201000-50201600	Active TSS	Aorta	Aorta
27	chr2:50201000-50201600	Active TSS	Colon Smooth Muscle	Colon
28	chr2:50201000-50201600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr2:50201000-50201600	Active TSS	Fetal Intestine Large	intestine
30	chr2:50201000-50201600	Active TSS	Fetal Thymus	thymus
31	chr2:50201000-50201600	Active TSS	Left Ventricle	heart
32	chr2:50201000-50201600	Active TSS	Thymus	Thymus
33	chr2:50201000-50201600	Active TSS	A549	lung
34	chr2:50201000-50201800	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr2:50201000-50201800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:50201000-50201800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:50201000-50201800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:50201000-50201800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:50201000-50201800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:50201000-50201800	Active TSS	Brain Substantia Nigra	brain
41	chr2:50201000-50201800	Active TSS	Fetal Brain Male	brain
42	chr2:50201000-50201800	Active TSS	Fetal Muscle Trunk	muscle
43	chr2:50201000-50201800	Active TSS	Fetal Stomach	stomach
44	chr2:50201000-50201800	Active TSS	Stomach Smooth Muscle	stomach
45	chr2:50201000-50201800	Active TSS	NH-A	brain
46	chr2:50201000-50202000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr2:50201200-50201600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
48	chr2:50201200-50201600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:50201200-50201600	Active TSS	Primary T cells from cord blood	blood
50	chr2:50201200-50201600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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