Variant report

Variant	rs4970702
Chromosome Location	chr1:92944994-92944995
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92943106..92945149-chr1:92950774..92953429,2	K562	blood:
2	chr1:92940468..92943663-chr1:92944026..92947261,3	K562	blood:

Variant related genes	Relation type
ENSG00000162676	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs1034218	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs1034219	0.82[CHB][hapmap]
rs1059267	0.93[EUR][1000 genomes]
rs1059268	0.93[EUR][1000 genomes]
rs10735779	0.82[CHB][hapmap]
rs10735781	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap]
rs10735782	0.82[CHB][hapmap]
rs10747445	0.82[CHB][hapmap]
rs10747446	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.80[EUR][1000 genomes]
rs10747448	0.82[CHB][hapmap]
rs10747449	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10747450	0.82[CHB][hapmap]
rs10782912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10782922	0.82[CHB][hapmap]
rs10782936	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs10782937	0.81[EUR][1000 genomes]
rs10782940	0.82[CHB][hapmap]
rs10874710	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs10874711	0.95[CEU][hapmap];0.85[CHB][hapmap];0.87[EUR][1000 genomes]
rs10874715	0.82[CHB][hapmap]
rs10874716	0.82[CHB][hapmap]
rs10874724	0.85[EUR][1000 genomes]
rs10874725	0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs10874726	0.83[EUR][1000 genomes]
rs10874727	0.91[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs10874728	0.82[CHB][hapmap]
rs10874729	0.82[CHB][hapmap]
rs10874731	0.82[CHB][hapmap]
rs11164601	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164778	0.82[CHB][hapmap]
rs11164785	0.83[EUR][1000 genomes]
rs11164791	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11164796	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs12025792	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs12046739	0.82[CHB][hapmap]
rs1325434	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[EUR][1000 genomes]
rs1359490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1408916	0.82[CHB][hapmap]
rs1415294	0.82[CHB][hapmap]
rs1415295	0.82[CHB][hapmap]
rs1537498	0.82[CHB][hapmap]
rs1538029	0.82[CHB][hapmap]
rs1556562	0.82[CHB][hapmap]
rs1556564	0.82[CHB][hapmap]
rs1556565	0.82[CHB][hapmap]
rs1570837	0.82[CHB][hapmap]
rs1886682	0.82[CHB][hapmap]
rs1886683	0.82[CHB][hapmap]
rs1886684	0.95[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1932965	1.00[CHB][hapmap]
rs2027059	0.82[CHB][hapmap]
rs2027060	0.82[CHB][hapmap]
rs2039452	0.82[CHB][hapmap]
rs2050597	0.82[CHB][hapmap]
rs2095268	0.82[CHB][hapmap]
rs2151577	0.82[CHB][hapmap]
rs2391164	0.82[CHB][hapmap]
rs2893217	0.82[CHB][hapmap]
rs3903212	0.95[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs3928821	0.82[CHB][hapmap]
rs3936944	0.82[EUR][1000 genomes]
rs3936945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3936946	1.00[CHB][hapmap]
rs4000736	0.85[EUR][1000 genomes]
rs4294422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs4294424	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap]
rs4484938	0.93[EUR][1000 genomes]
rs4565725	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4568842	0.82[CHB][hapmap]
rs4847181	0.82[CHB][hapmap]
rs4847232	0.82[CHB][hapmap]
rs4847247	0.82[CHB][hapmap]
rs4847280	0.82[CHB][hapmap]
rs4847305	0.82[CHB][hapmap]
rs4847327	0.82[CHB][hapmap]
rs4847377	0.82[CHB][hapmap]
rs4847432	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4970700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970703	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970707	0.90[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs4970709	0.82[CHB][hapmap]
rs4970710	0.82[CHB][hapmap]
rs4970712	0.82[CHB][hapmap]
rs4970714	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6422512	0.82[CHB][hapmap]
rs6422515	0.82[CHB][hapmap]
rs6603976	0.93[EUR][1000 genomes]
rs6603979	0.82[CHB][hapmap]
rs6603981	0.82[CHB][hapmap]
rs6603982	0.82[CHB][hapmap]
rs6603984	0.82[CHB][hapmap]
rs6603985	0.82[CHB][hapmap]
rs6603986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603987	0.82[CHB][hapmap]
rs6603988	0.82[CHB][hapmap]
rs6603989	0.86[EUR][1000 genomes]
rs6603990	0.82[CHB][hapmap]
rs6603992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603993	0.82[CHB][hapmap]
rs6603994	0.82[CHB][hapmap]
rs6603995	0.82[CHB][hapmap]
rs6603997	0.95[CEU][hapmap];0.85[CHB][hapmap];0.83[EUR][1000 genomes]
rs6603999	0.82[CHB][hapmap]
rs6660962	0.90[EUR][1000 genomes]
rs6671114	0.82[CHB][hapmap]
rs6675246	0.82[CHB][hapmap]
rs6682801	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs6692187	0.82[CHB][hapmap]
rs6695638	0.86[EUR][1000 genomes]
rs6696173	0.82[CHB][hapmap]
rs6697491	0.86[EUR][1000 genomes]
rs6701130	0.82[CHB][hapmap]
rs6703440	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs722356	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes]
rs7417452	0.85[EUR][1000 genomes]
rs7513775	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7514156	0.94[EUR][1000 genomes]
rs7514716	0.82[CHB][hapmap]
rs7515577	0.82[CHB][hapmap]
rs7520630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521752	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7529332	0.82[CHB][hapmap]
rs7529630	0.82[CHB][hapmap]
rs7530780	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap]
rs7535490	0.85[EUR][1000 genomes]
rs7540564	0.94[EUR][1000 genomes]
rs7541942	0.85[EUR][1000 genomes]
rs7545318	0.82[CHB][hapmap]
rs7553367	0.82[CHB][hapmap]
rs7556243	0.82[CHB][hapmap]
rs912795	0.82[CHB][hapmap]
rs912796	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[EUR][1000 genomes]
rs914966	0.82[CHB][hapmap]
rs942753	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963043	0.82[CHB][hapmap]
rs963044	0.82[CHB][hapmap]
rs9651256	0.82[CHB][hapmap]
rs989653	0.82[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523354	chr1:92931263-93064823	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4970702	FAM69A	cis	cerebellum	SCAN
rs4970702	MTF2	cis	cerebellum	SCAN
rs4970702	EPHX4	cis	parietal	SCAN
rs4970702	RPL5	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92925600-92946000	Weak transcription	Right Atrium	heart
2	chr1:92939400-92945800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:92939800-92945200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:92940000-92947400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr1:92941800-92946000	Weak transcription	Gastric	stomach
6	chr1:92942000-92945600	Weak transcription	Pancreas	Pancrea
7	chr1:92942600-92947400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:92942600-92947600	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr1:92942800-92947200	Weak transcription	Primary B cells from cord blood	blood
10	chr1:92942800-92947600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:92943200-92947000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:92943200-92949200	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr1:92943400-92945600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:92943400-92949200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
15	chr1:92943600-92946000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:92943800-92946600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr1:92943800-92946800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:92944000-92945200	Strong transcription	HepG2	liver
19	chr1:92944000-92945800	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:92944000-92946000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr1:92944000-92946800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:92944200-92945200	Enhancers	GM12878-XiMat	blood
23	chr1:92944200-92946800	Strong transcription	Primary hematopoietic stem cells	blood
24	chr1:92944400-92946000	Strong transcription	Primary T cells from cord blood	blood
25	chr1:92944400-92946800	ZNF genes & repeats	Spleen	Spleen
26	chr1:92944600-92945600	Genic enhancers	Thymus	Thymus
27	chr1:92944600-92945800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:92944800-92945000	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
29	chr1:92944800-92945400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr1:92944800-92945600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:92944800-92946800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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