Variant report

Variant	rs4971883
Chromosome Location	chr2:50201383-50201384
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	GABPA	chr2:50201180-50201629	A549	lung:	n/a	n/a
2	CTCF	chr2:50201354-50201402	MCF-7	breast:	n/a	n/a
3	NRF1	chr2:50200942-50201617	SK-N-SH	brain:	n/a	n/a
4	GABPA	chr2:50201248-50201488	HepG2	liver:	n/a	n/a
5	MAX	chr2:50201283-50201469	A549	lung:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
6	USF2	chr2:50201277-50201527	GM12878	blood:	n/a	n/a
7	ELF1	chr2:50201257-50201496	GM12878	blood:	n/a	n/a
8	POLR2A	chr2:50201225-50201536	A549	lung:	n/a	n/a
9	EP300	chr2:50201124-50201533	SK-N-SH_RA	brain:	n/a	n/a
10	FOXP2	chr2:50201240-50201525	PFSK-1	brain:	n/a	n/a
11	USF1	chr2:50201095-50201541	SK-N-SH_RA	brain:	n/a	chr2:50201350-50201361
12	POLR2A	chr2:50201020-50201618	U87	brain:	n/a	n/a
13	TAF1	chr2:50201279-50201478	SK-N-SH	brain:	n/a	n/a
14	NFYB	chr2:50201158-50201554	GM12878	blood:	n/a	n/a
15	PBX3	chr2:50201006-50201621	SK-N-SH	brain:	n/a	chr2:50201346-50201355
16	POLR2A	chr2:50201107-50201635	U87	brain:	n/a	n/a
17	MAX	chr2:50201154-50201560	H1-hESC	embryonic stem cell:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
18	MAX	chr2:50201047-50201596	SK-N-SH	brain:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
19	USF1	chr2:50201042-50201611	SK-N-SH_RA	brain:	n/a	chr2:50201350-50201361
20	USF1	chr2:50201120-50201565	A549	lung:	n/a	chr2:50201350-50201361
21	GABPA	chr2:50201148-50201629	A549	lung:	n/a	n/a
22	USF1	chr2:50201107-50201581	H1-hESC	embryonic stem cell:	n/a	chr2:50201350-50201361
23	ATF3	chr2:50201231-50201453	GM12878	blood:	n/a	n/a
24	USF1	chr2:50201198-50201491	HepG2	liver:	n/a	chr2:50201350-50201361
25	POLR2A	chr2:50201082-50201653	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr2:50201271-50201486	MCF-7	breast:	n/a	n/a
27	REST	chr2:50199676-50201874	H1-neurons	neurons:	n/a	chr2:50200054-50200067
28	USF1	chr2:50201245-50201444	HepG2	liver:	n/a	chr2:50201350-50201361
29	FOXP2	chr2:50201193-50201591	SK-N-MC	brain:	n/a	n/a
30	USF1	chr2:50201092-50201558	A549	lung:	n/a	chr2:50201350-50201361
31	GATA3	chr2:50200994-50201673	SK-N-SH	brain:	n/a	chr2:50201391-50201401
32	SETDB1	chr2:50201066-50201638	U2OS	brain:	n/a	n/a
33	POLR2A	chr2:50200659-50201665	H1-neurons	neurons:	n/a	n/a
34	USF1	chr2:50201201-50201484	A549	lung:	n/a	chr2:50201350-50201361
35	KAP1	chr2:50201064-50201521	U2OS	brain:	n/a	n/a
36	GATA3	chr2:50200950-50201598	SH-SY5Y	brain:	n/a	chr2:50201391-50201401
37	FOXA2	chr2:50201291-50201557	A549	lung:	n/a	n/a
38	POLR2A	chr2:50201235-50201467	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr2:50201242-50201442	GM12878	blood:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
40	ATF3	chr2:50201138-50201446	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAX	chr2:50201214-50201468	NB4	blood:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
42	MAX	chr2:50201124-50201646	A549	lung:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
43	POLR2A	chr2:50201333-50201507	SK-N-SH	brain:	n/a	n/a
44	POLR2A	chr2:50200642-50201618	H1-neurons	neurons:	n/a	n/a
45	MYC	chr2:50201326-50201462	MCF-7	breast:	n/a	chr2:50201352-50201361 chr2:50201352-50201361
46	USF1	chr2:50200960-50201633	H1-hESC	embryonic stem cell:	n/a	chr2:50201350-50201361
47	EP300	chr2:50201159-50201524	SK-N-SH_RA	brain:	n/a	n/a
48	USF1	chr2:50201127-50201529	A549	lung:	n/a	chr2:50201350-50201361
49	USF2	chr2:50201162-50201549	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr2:50201145-50201680	SK-N-MC	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:50201382-50201432	BE2_C	brain:	n/a
2	chr2:50201382-50201432	SK-N-SH_RA	brain:	n/a
3	chr2:50201382-50201432	HRCEpiC	kidney:	n/a
4	chr2:50201382-50201432	AG10803	skin:	n/a
5	chr2:50201382-50201432	K562	blood:	n/a
6	chr2:50201382-50201432	MCF-7	breast:	n/a
7	chr2:50201382-50201432	IMR90	lung:	fetal
8	chr2:50201382-50201432	ovcar-3	ovarian:	n/a
9	chr2:50201382-50201432	SKMC	muscle:	n/a
10	chr2:50201382-50201432	SAEC	small airway:	n/a
11	chr2:50201382-50201432	LNCaP	prostate:	n/a
12	chr2:50201382-50201432	RPTEC	kidney:	n/a
13	chr2:50201382-50201432	AoSMC	blood vessel:	n/a
14	chr2:50201382-50201432	NB4	blood:	n/a
15	chr2:50201382-50201432	AG04449	skin:	fetal
16	chr2:50201382-50201432	HMEC	breast:	n/a
17	chr2:50201382-50201432	HAEpiC	amniotic membrane:	n/a
18	chr2:50201382-50201432	HRE	kidney:	n/a
19	chr2:50201382-50201432	AG09319	gingival:	n/a
20	chr2:50201382-50201432	HRPEpiC	eye:	n/a
21	chr2:50201382-50201432	HIPEpiC	eye:	n/a
22	chr2:50201382-50201432	H1-hESC	embryonic stem cell:	embryo
23	chr2:50201382-50201432	HCM	heart:	n/a
24	chr2:50201382-50201432	GM12892	blood:	n/a
25	chr2:50201382-50201432	Caco-2	colon:	n/a
26	chr2:50201382-50201432	Hela-S3	cervix:	n/a
27	chr2:50201382-50201432	HCF	heart:	n/a
28	chr2:50201382-50201432	SK-N-MC	brain:	n/a
29	chr2:50201382-50201432	ProgFib	skin:	n/a
30	chr2:50201382-50201432	HCT-116	colon:	n/a
31	chr2:50201382-50201432	HEEpiC	esophagus:	n/a
32	chr2:50201382-50201432	NH-A	brain:	n/a
33	chr2:50201382-50201432	ECC-1	luminal epithelium:	n/a
34	chr2:50201382-50201432	BJ	skin:	n/a
35	chr2:50201382-50201432	PFSK-1	brain:	n/a
36	chr2:50201382-50201432	Hepatocyte	liver:	n/a
37	chr2:50201382-50201432	HPAEpiC	pulmonary alveolar:	n/a
38	chr2:50201382-50201432	HL-60	blood:	n/a
39	chr2:50201382-50201432	HEK293	kidney:	embryo
40	chr2:50201382-50201432	HepG2	liver:	n/a
41	chr2:50201382-50201432	SK-N-SH	brain:	n/a
42	chr2:50201382-50201432	AG09309	skin:	n/a
43	chr2:50201382-50201432	GM12891	blood:	n/a
44	chr2:50201382-50201432	Jurkat	blood:	n/a
45	chr2:50201382-50201432	NHDF-neo	bronchial:	n/a
46	chr2:50201382-50201432	HCPEpiC	choroid plexus:	n/a
47	chr2:50201382-50201432	A549	lung:	n/a
48	chr2:50201382-50201432	HUVEC	blood vessel:	n/a
49	chr2:50201382-50201432	PrEC	prostate:	n/a
50	chr2:50201382-50201432	GM06990	blood:	n/a

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

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10173664	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10185922	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10192677	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10196324	0.96[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11125281	0.89[CEU][hapmap]
rs12713081	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12713082	0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13025736	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1421579	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1421580	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1421599	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1435090	0.89[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1469004	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1543823	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2216521	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6706472	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4971883	SOCS5	cis	parietal	SCAN

Chromatin state (count:98 , 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	chr2:50199200-50201400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:50199200-50201400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:50199600-50201600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:50199600-50201800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr2:50199800-50201800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:50199800-50201800	Active TSS	Brain Anterior Caudate	brain
8	chr2:50199800-50201800	Active TSS	Brain Cingulate Gyrus	brain
9	chr2:50200000-50201800	Active TSS	Fetal Brain Female	brain
10	chr2:50200600-50201800	Active TSS	Brain Germinal Matrix	brain
11	chr2:50200600-50201800	Active TSS	Fetal Kidney	kidney
12	chr2:50200800-50201400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:50200800-50201800	Active TSS	Brain Hippocampus Middle	brain
14	chr2:50200800-50201800	Active TSS	Fetal Intestine Small	intestine
15	chr2:50200800-50201800	Active TSS	Right Atrium	heart
16	chr2:50200800-50205600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:50201000-50201400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
18	chr2:50201000-50201400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr2:50201000-50201400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:50201000-50201400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:50201000-50201400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:50201000-50201400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:50201000-50201400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr2:50201000-50201400	Flanking Active TSS	Fetal Lung	lung
25	chr2:50201000-50201400	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr2:50201000-50201400	Active TSS	Rectal Smooth Muscle	rectum
27	chr2:50201000-50201600	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr2:50201000-50201600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr2:50201000-50201600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr2:50201000-50201600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr2:50201000-50201600	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr2:50201000-50201600	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr2:50201000-50201600	Active TSS	Primary B cells from cord blood	blood
34	chr2:50201000-50201600	Active TSS	Primary T cells fromperipheralblood	blood
35	chr2:50201000-50201600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr2:50201000-50201600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr2:50201000-50201600	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr2:50201000-50201600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr2:50201000-50201600	Active TSS	Aorta	Aorta
40	chr2:50201000-50201600	Active TSS	Colon Smooth Muscle	Colon
41	chr2:50201000-50201600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr2:50201000-50201600	Active TSS	Fetal Intestine Large	intestine
43	chr2:50201000-50201600	Active TSS	Fetal Thymus	thymus
44	chr2:50201000-50201600	Active TSS	Left Ventricle	heart
45	chr2:50201000-50201600	Active TSS	Thymus	Thymus
46	chr2:50201000-50201600	Active TSS	A549	lung
47	chr2:50201000-50201800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:50201000-50201800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:50201000-50201800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:50201000-50201800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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