Variant report

Variant	rs4294422
Chromosome Location	chr1:93104655-93104656
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	chr1:92762843..92765397-chr1:93103121..93105425,2	K562	blood:

Variant related genes	Relation type
ENSG00000174842	Chromatin interaction
ENSG00000122484	Chromatin interaction

Extended variants
information (count: 208 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:205)

rs_ID	r²[population]
rs1003116	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs10218670	0.82[CHB][hapmap]
rs1034218	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs1034219	0.82[CHB][hapmap]
rs1059267	0.84[EUR][1000 genomes]
rs1059268	0.84[EUR][1000 genomes]
rs10735779	0.82[CHB][hapmap]
rs10735781	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs10735782	0.82[CHB][hapmap]
rs10747445	0.82[CHB][hapmap]
rs10747446	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[TSI][hapmap];0.92[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];0.85[EUR][1000 genomes]
rs10782922	0.82[CHB][hapmap]
rs10782936	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs10782937	0.92[EUR][1000 genomes]
rs10782940	0.82[CHB][hapmap]
rs10782941	0.84[EUR][1000 genomes]
rs10874710	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs10874711	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[EUR][1000 genomes]
rs10874715	0.82[CHB][hapmap]
rs10874716	0.82[CHB][hapmap]
rs10874724	0.90[EUR][1000 genomes]
rs10874725	0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs10874726	0.93[EUR][1000 genomes]
rs10874727	0.91[CEU][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes]
rs10874728	0.82[CHB][hapmap]
rs10874729	0.82[CHB][hapmap]
rs10874731	0.82[CHB][hapmap]
rs10874732	0.84[EUR][1000 genomes]
rs10874733	0.84[EUR][1000 genomes]
rs10874736	0.82[EUR][1000 genomes]
rs11164601	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11164608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11164778	0.82[CHB][hapmap]
rs11164785	0.86[EUR][1000 genomes]
rs11164789	0.88[EUR][1000 genomes]
rs11164791	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs11164796	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs11164804	0.82[CHB][hapmap]
rs11164808	0.82[CHB][hapmap]
rs12025792	0.95[CEU][hapmap];0.85[CHB][hapmap];0.94[EUR][1000 genomes]
rs12046739	0.82[CHB][hapmap]
rs12123935	0.82[EUR][1000 genomes]
rs1325434	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs1337107	1.00[CHB][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs1337109	0.82[CHB][hapmap]
rs1359490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs1408916	0.82[CHB][hapmap]
rs1415294	0.82[CHB][hapmap]
rs1415295	0.82[CHB][hapmap]
rs1535372	0.86[CEU][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];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs1932965	1.00[CHB][hapmap]
rs1932966	0.82[CHB][hapmap]
rs2027059	0.82[CHB][hapmap]
rs2027060	0.82[CHB][hapmap]
rs2039452	0.82[CHB][hapmap]
rs2050597	0.82[CHB][hapmap]
rs2065915	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2065916	0.82[CHB][hapmap]
rs2095268	0.82[CHB][hapmap]
rs2107519	0.81[EUR][1000 genomes]
rs2107520	0.82[CHB][hapmap]
rs2107521	0.82[CHB][hapmap]
rs2151577	0.82[CHB][hapmap]
rs2158446	0.82[CHB][hapmap]
rs2180977	0.82[CHB][hapmap]
rs2391164	0.82[CHB][hapmap]
rs2391196	0.82[CHB][hapmap]
rs2391199	0.82[CHB][hapmap]
rs2893217	0.82[CHB][hapmap]
rs35029291	0.85[EUR][1000 genomes]
rs35054144	0.82[CHB][hapmap]
rs3790445	0.82[CHB][hapmap]
rs3790446	0.82[CHB][hapmap]
rs3903212	0.95[CEU][hapmap];0.85[CHB][hapmap];0.86[EUR][1000 genomes]
rs3928821	0.82[CHB][hapmap]
rs3936944	0.94[EUR][1000 genomes]
rs3936945	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]
rs3936946	1.00[CHB][hapmap]
rs4294424	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs4480368	0.83[EUR][1000 genomes]
rs4484938	0.81[EUR][1000 genomes]
rs4525048	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4565725	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4568842	0.82[CHB][hapmap]
rs4847181	0.82[CHB][hapmap]
rs4847232	0.82[CHB][hapmap]
rs4847247	0.82[CHB][hapmap]
rs4847266	0.82[CHB][hapmap]
rs4847267	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs4847280	0.82[CHB][hapmap]
rs4847305	0.82[CHB][hapmap]
rs4847306	0.81[EUR][1000 genomes]
rs4847311	0.84[EUR][1000 genomes]
rs4847327	0.82[CHB][hapmap]
rs4847377	0.82[CHB][hapmap]
rs4847432	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes]
rs4970700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4970702	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]
rs4970703	0.85[EUR][1000 genomes]
rs4970707	0.90[CEU][hapmap];0.85[CHB][hapmap];0.86[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];0.84[EUR][1000 genomes]
rs6422512	0.82[CHB][hapmap]
rs6422515	0.82[CHB][hapmap]
rs6603976	0.82[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[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6603987	0.82[CHB][hapmap]
rs6603988	0.82[CHB][hapmap]
rs6603989	0.90[EUR][1000 genomes]
rs6603990	0.82[CHB][hapmap]
rs6603992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.93[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];0.88[EUR][1000 genomes]
rs6603999	0.82[CHB][hapmap]
rs6604003	0.82[CHB][hapmap]
rs6604007	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs6604008	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6604010	0.82[CHB][hapmap]
rs6604013	0.80[EUR][1000 genomes]
rs6604014	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs6604015	0.82[CHB][hapmap]
rs6604018	0.82[CHB][hapmap]
rs6660136	0.83[EUR][1000 genomes]
rs6660962	0.86[EUR][1000 genomes]
rs6661600	0.82[CHB][hapmap]
rs6666831	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs6671114	0.82[CHB][hapmap]
rs6671421	0.82[CHB][hapmap]
rs6675246	0.82[CHB][hapmap]
rs6675753	0.82[EUR][1000 genomes]
rs6680578	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs6682801	0.95[CEU][hapmap];0.85[CHB][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6685705	0.82[CHB][hapmap]
rs6692187	0.82[CHB][hapmap]
rs6695638	0.87[EUR][1000 genomes]
rs6696173	0.82[CHB][hapmap]
rs6696636	0.82[CHB][hapmap]
rs6697491	0.90[EUR][1000 genomes]
rs6701130	0.82[CHB][hapmap]
rs6703440	0.81[EUR][1000 genomes]
rs6703467	0.82[CHB][hapmap]
rs722356	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs7416169	0.82[CHB][hapmap]
rs7417452	0.89[EUR][1000 genomes]
rs7418336	0.82[CEU][hapmap];0.85[CHB][hapmap];0.85[TSI][hapmap]
rs7513775	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs7513815	0.82[CHB][hapmap]
rs7514156	0.82[EUR][1000 genomes]
rs7514334	0.90[EUR][1000 genomes]
rs7514716	0.82[CHB][hapmap]
rs7515577	0.82[CHB][hapmap]
rs7516141	0.82[CHB][hapmap]
rs7520630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs7521752	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs7526582	0.82[CHB][hapmap]
rs7529332	0.82[CHB][hapmap]
rs7529630	0.82[CHB][hapmap]
rs7530780	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs7535490	0.90[EUR][1000 genomes]
rs7540407	0.82[CHB][hapmap]
rs7540564	0.81[EUR][1000 genomes]
rs7541942	0.86[EUR][1000 genomes]
rs7543327	0.82[CHB][hapmap]
rs7545318	0.82[CHB][hapmap]
rs7546197	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7549844	0.82[CHB][hapmap]
rs7553367	0.82[CHB][hapmap]
rs7556243	0.82[CHB][hapmap]
rs911523	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs912795	0.82[CHB][hapmap]
rs912796	0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[EUR][1000 genomes]
rs914966	0.82[CHB][hapmap]
rs927339	0.82[CHB][hapmap]
rs932637	0.82[CHB][hapmap]
rs942753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9439920	0.82[CHB][hapmap]
rs945724	0.82[CHB][hapmap]
rs963043	0.82[CHB][hapmap]
rs963044	0.82[CHB][hapmap]
rs9651256	0.82[CHB][hapmap]
rs976208	0.82[CHB][hapmap]
rs989653	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830603	chr1:93003657-93172206	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv1794348	chr1:93090476-93192932	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv1802611	chr1:93090476-93219907	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4294422	FAM69A	cis	cerebellum	SCAN
rs4294422	RPL5	cis	parietal	SCAN
rs4294422	MTF2	cis	cerebellum	SCAN
rs4294422	EPHX4	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93052000-93119400	Weak transcription	NHEK	skin
2	chr1:93053600-93166200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:93062000-93118800	Weak transcription	HMEC	breast
4	chr1:93065200-93118600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr1:93065800-93119600	Weak transcription	NH-A	brain
6	chr1:93066800-93114600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:93068600-93112600	Weak transcription	Brain Substantia Nigra	brain
8	chr1:93069600-93119600	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:93082600-93108600	Weak transcription	Psoas Muscle	Psoas
10	chr1:93083600-93106400	Weak transcription	Pancreas	Pancrea
11	chr1:93089800-93114200	Weak transcription	HSMM	muscle
12	chr1:93098400-93205400	Weak transcription	NHLF	lung
13	chr1:93100600-93118600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:93101200-93114600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:93101200-93118600	Weak transcription	Aorta	Aorta
16	chr1:93101200-93118800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:93101400-93104800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:93101400-93104800	Weak transcription	Ovary	ovary
19	chr1:93101400-93118200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:93101400-93118200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:93101400-93118200	Weak transcription	Left Ventricle	heart
22	chr1:93101400-93118400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:93101400-93118400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:93101400-93118400	Weak transcription	Fetal Intestine Small	intestine
25	chr1:93101400-93118400	Weak transcription	Fetal Stomach	stomach
26	chr1:93101400-93118600	Weak transcription	Lung	lung
27	chr1:93101400-93118600	Weak transcription	Right Ventricle	heart
28	chr1:93101400-93118800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:93101400-93119000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:93101400-93119000	Weak transcription	Gastric	stomach
31	chr1:93101600-93105400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr1:93101600-93118400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:93101600-93118600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:93101600-93120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:93101600-93163600	Weak transcription	Colonic Mucosa	Colon
36	chr1:93101800-93106000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:93101800-93106400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:93101800-93106400	Weak transcription	Fetal Kidney	kidney
39	chr1:93101800-93110600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:93101800-93118200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:93101800-93118600	Weak transcription	HSMMtube	muscle
42	chr1:93101800-93119200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr1:93101800-93119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:93102000-93106400	Weak transcription	Liver	Liver
45	chr1:93102000-93106400	Weak transcription	Fetal Lung	lung
46	chr1:93102000-93109000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:93102000-93112400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:93102000-93114400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:93102000-93115200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:93102000-93117600	Weak transcription	Fetal Intestine Large	intestine

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