Variant report

Variant	rs6719571
Chromosome Location	chr2:50201744-50201745
allele	C/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	REST	chr2:50199676-50201874	H1-neurons	neurons:	n/a	chr2:50200054-50200067
2	MXI1	chr2:50199140-50201817	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:114)

rs_ID	r²[population]
rs10495991	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495992	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10495993	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10495994	0.96[CEU][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1159136	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1159137	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11887101	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11889551	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896576	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11896677	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.96[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11897428	0.92[CEU][hapmap]
rs11899849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12615365	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620898	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363025	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1363026	0.92[CEU][hapmap]
rs1363027	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs1363031	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs1363032	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs1363038	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1369294	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1421568	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs1421582	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1421583	1.00[CEU][hapmap];0.85[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1421584	1.00[CEU][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1421585	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1592722	0.92[CEU][hapmap];0.85[YRI][hapmap]
rs1592723	0.92[CEU][hapmap]
rs1592725	0.92[CEU][hapmap]
rs1592726	0.92[CEU][hapmap]
rs1592727	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs17439468	0.81[CEU][hapmap]
rs17440201	0.92[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17441066	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17441242	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17441396	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17492942	0.92[CEU][hapmap]
rs17493005	0.92[CEU][hapmap]
rs17493081	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17493116	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17493390	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17493439	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17494124	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1836545	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs1865488	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1865489	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1895126	1.00[CEU][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1895127	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1895129	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2112073	0.94[ASW][hapmap];0.96[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2193866	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2193867	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2216522	1.00[CEU][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2351146	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2351148	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2882594	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3796036	0.84[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4404319	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56889513	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57193820	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57707897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58564477	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59032342	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59781568	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60267441	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61073961	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61405508	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62132489	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62132490	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62134599	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62134600	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62134607	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62134608	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62134651	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62134654	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62134655	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62134656	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62134657	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545138	0.92[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs6545140	1.00[CEU][hapmap]
rs6545142	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6710767	0.96[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6722600	0.92[CEU][hapmap]
rs6733024	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6741686	0.92[CEU][hapmap]
rs6747457	0.92[CEU][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6754304	0.92[CEU][hapmap]
rs6755887	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72887815	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72887817	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72887819	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72887820	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72887870	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72887883	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7421423	0.92[CEU][hapmap]
rs7426139	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7559968	0.85[AMR][1000 genomes]
rs7563039	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7563354	1.00[CEU][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7565688	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7565706	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7569404	0.92[CEU][hapmap];0.86[YRI][hapmap]
rs7569617	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573331	0.81[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7573338	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573588	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7587669	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7590237	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7591097	0.92[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7595904	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7599940	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7603788	1.00[CEU][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7604126	0.81[CEU][hapmap]
rs9941548	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[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
rs6719571	SOCS5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50198800-50201800	Active TSS	Brain Angular Gyrus	brain
2	chr2:50199600-50201800	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr2:50199800-50201800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:50199800-50201800	Active TSS	Brain Anterior Caudate	brain
5	chr2:50199800-50201800	Active TSS	Brain Cingulate Gyrus	brain
6	chr2:50200000-50201800	Active TSS	Fetal Brain Female	brain
7	chr2:50200600-50201800	Active TSS	Brain Germinal Matrix	brain
8	chr2:50200600-50201800	Active TSS	Fetal Kidney	kidney
9	chr2:50200800-50201800	Active TSS	Brain Hippocampus Middle	brain
10	chr2:50200800-50201800	Active TSS	Fetal Intestine Small	intestine
11	chr2:50200800-50201800	Active TSS	Right Atrium	heart
12	chr2:50200800-50205600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:50201000-50201800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr2:50201000-50201800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:50201000-50201800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:50201000-50201800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:50201000-50201800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:50201000-50201800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:50201000-50201800	Active TSS	Brain Substantia Nigra	brain
20	chr2:50201000-50201800	Active TSS	Fetal Brain Male	brain
21	chr2:50201000-50201800	Active TSS	Fetal Muscle Trunk	muscle
22	chr2:50201000-50201800	Active TSS	Fetal Stomach	stomach
23	chr2:50201000-50201800	Active TSS	Stomach Smooth Muscle	stomach
24	chr2:50201000-50201800	Active TSS	NH-A	brain
25	chr2:50201000-50202000	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr2:50201200-50201800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:50201200-50201800	Active TSS	Primary hematopoietic stem cells	blood
28	chr2:50201200-50201800	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr2:50201200-50201800	Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr2:50201200-50201800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr2:50201200-50201800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:50201200-50201800	Active TSS	Fetal Heart	heart
33	chr2:50201200-50205400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr2:50201400-50201800	Active TSS	H1 Cell Line	embryonic stem cell
35	chr2:50201400-50201800	Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr2:50201400-50201800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:50201400-50201800	Active TSS	Fetal Muscle Leg	muscle
38	chr2:50201600-50201800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr2:50201600-50201800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr2:50201600-50201800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:50201600-50201800	Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr2:50201600-50201800	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr2:50201600-50201800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr2:50201600-50201800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr2:50201600-50201800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:50201600-50201800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr2:50201600-50201800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:50201600-50201800	Enhancers	Adipose Nuclei	Adipose
49	chr2:50201600-50201800	Flanking Active TSS	Fetal Lung	lung
50	chr2:50201600-50205400	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links