Variant report

Variant	rs704829
Chromosome Location	chr1:176150152-176150153
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176148340..176150174-chr1:176160183..176162598,2	K562	blood:
2	chr1:176149132..176153011-chr1:176153714..176156384,3	K562	blood:
3	chr1:176148670..176151636-chr1:176153714..176157019,4	K562	blood:
4	chr1:176149685..176152103-chr1:176175272..176177235,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143207	Chromatin interaction
ENSG00000236021	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10753117	0.91[JPT][hapmap]
rs10798434	0.86[JPT][hapmap]
rs10798442	0.91[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10798446	0.86[JPT][hapmap]
rs10913117	0.86[JPT][hapmap]
rs10913118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10913135	0.85[JPT][hapmap]
rs10913137	0.86[JPT][hapmap]
rs10913143	0.86[JPT][hapmap]
rs10913144	0.86[JPT][hapmap]
rs10913147	0.86[JPT][hapmap]
rs10913152	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11810706	0.95[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs12029090	0.89[JPT][hapmap]
rs12033847	0.91[JPT][hapmap]
rs12049077	0.86[JPT][hapmap]
rs12117377	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138008	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12404596	0.91[JPT][hapmap]
rs12729524	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs12758275	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16849486	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs17354120	0.86[JPT][hapmap]
rs1858537	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs191606	0.81[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes]
rs1974142	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2039230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2102479	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2175177	0.90[JPT][hapmap]
rs2175178	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2455730	0.81[AMR][1000 genomes]
rs2455732	0.81[AMR][1000 genomes]
rs2455749	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2457418	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2481628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2481633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2481655	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs2481662	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2487144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2502823	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2502831	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2502845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2504493	0.86[JPT][hapmap]
rs2504501	0.81[AMR][1000 genomes]
rs35907544	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3962371	0.86[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4298694	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs482228	0.81[EUR][1000 genomes]
rs501142	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513354	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534088	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs542742	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs596859	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs659279	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678628	0.86[JPT][hapmap]
rs6678812	0.86[JPT][hapmap]
rs668154	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687280	0.81[EUR][1000 genomes]
rs6697860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700932	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs670143	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs679728	0.86[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs704834	0.86[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs71645275	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7517503	0.86[JPT][hapmap]
rs7535769	0.86[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7549160	0.90[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs791743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791746	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791747	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs791750	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791752	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs791753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs813180	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs944365	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv872565	chr1:176058782-176172795	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs704829	EME2	trans	cerebellum	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:176065600-176154800	Weak transcription	Aorta	Aorta
2	chr1:176070400-176151400	Weak transcription	Pancreas	Pancrea
3	chr1:176100800-176153200	Weak transcription	Colonic Mucosa	Colon
4	chr1:176110600-176164000	Weak transcription	NHLF	lung
5	chr1:176126400-176168800	Weak transcription	Small Intestine	intestine
6	chr1:176127000-176174000	Weak transcription	Colon Smooth Muscle	Colon
7	chr1:176127200-176153400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:176127400-176153400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr1:176127400-176155400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:176128000-176157800	Weak transcription	Spleen	Spleen
11	chr1:176128000-176175200	Weak transcription	Esophagus	oesophagus
12	chr1:176128400-176154600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:176128600-176155600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:176128800-176152800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:176128800-176152800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:176128800-176154200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:176132200-176154200	Weak transcription	NH-A	brain
18	chr1:176134400-176152800	Weak transcription	Brain Angular Gyrus	brain
19	chr1:176137400-176173000	Weak transcription	Right Ventricle	heart
20	chr1:176138200-176155800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:176138800-176155400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:176139000-176153800	Strong transcription	Dnd41	blood
23	chr1:176139800-176152600	Weak transcription	Brain Anterior Caudate	brain
24	chr1:176140000-176155800	Weak transcription	Fetal Brain Female	brain
25	chr1:176140000-176157800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr1:176140000-176168200	Weak transcription	Psoas Muscle	Psoas
27	chr1:176140200-176150200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:176140200-176152200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:176140800-176153600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:176140800-176155800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:176142200-176153400	Weak transcription	Fetal Heart	heart
32	chr1:176142200-176154400	Weak transcription	Fetal Kidney	kidney
33	chr1:176142800-176157800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr1:176142800-176162200	Weak transcription	HepG2	liver
35	chr1:176143000-176150600	Weak transcription	Fetal Intestine Small	intestine
36	chr1:176143000-176150600	Weak transcription	Thymus	Thymus
37	chr1:176143000-176151200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:176143000-176153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr1:176143000-176165800	Weak transcription	Lung	lung
40	chr1:176143600-176152400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:176143800-176153200	Weak transcription	HSMMtube	muscle
42	chr1:176144000-176172800	Weak transcription	HMEC	breast
43	chr1:176144200-176155600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr1:176144400-176152200	Weak transcription	NHEK	skin
45	chr1:176144400-176158200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:176144400-176170800	Weak transcription	K562	blood
47	chr1:176144400-176173400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr1:176144600-176151200	Weak transcription	Fetal Lung	lung
49	chr1:176144600-176168600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:176144800-176151400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links