Variant report

Variant	rs2948441
Chromosome Location	chr2:73825770-73825771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73821998..73823983-chr2:73825301..73826890,2	K562	blood:
2	chr2:73824033..73827858-chr2:73829276..73833224,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116127	Chromatin interaction

Extended variants
information (count: 138 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs10190002	1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs10192125	0.94[EUR][1000 genomes]
rs10197233	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1052161	0.87[JPT][hapmap]
rs1083920	0.87[EUR][1000 genomes]
rs1083922	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs10865398	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1091568	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11126407	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11126408	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11126409	0.87[EUR][1000 genomes]
rs11126411	0.83[CEU][hapmap]
rs11680056	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11683970	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11685372	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11689767	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12151671	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1246096	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1246105	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12478871	1.00[CEU][hapmap];0.80[YRI][hapmap]
rs12618600	0.92[CHB][hapmap];0.93[JPT][hapmap]
rs12620018	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs12620091	0.82[CHB][hapmap]
rs12620569	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12713783	0.94[EUR][1000 genomes]
rs13007306	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13007623	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13009035	0.89[ASN][1000 genomes]
rs13017182	0.92[CHB][hapmap]
rs1320374	0.87[JPT][hapmap]
rs1406105	0.91[CHB][hapmap];0.93[JPT][hapmap]
rs17349804	0.98[EUR][1000 genomes]
rs1852645	0.90[EUR][1000 genomes]
rs1852646	0.82[EUR][1000 genomes]
rs1852647	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs1879662	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1879666	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1881246	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1881247	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs1881248	0.94[EUR][1000 genomes]
rs2017116	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2037814	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes]
rs2280506	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2280507	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2421545	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2421546	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs2421581	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2421582	1.00[CHB][hapmap]
rs2421583	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs2421585	0.89[EUR][1000 genomes]
rs2421587	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2421589	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2421590	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421660	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421661	0.81[AMR][1000 genomes]
rs2421662	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2421667	0.92[ASN][1000 genomes]
rs2421668	0.92[CHB][hapmap]
rs2421669	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap]
rs2461691	0.82[EUR][1000 genomes]
rs2860579	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28708576	0.83[EUR][1000 genomes]
rs2947845	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs2950770	0.92[EUR][1000 genomes]
rs34719281	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3820700	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3980696	0.87[EUR][1000 genomes]
rs4241256	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4436991	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4443018	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4511748	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[EUR][1000 genomes]
rs4627598	0.84[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4637150	0.81[EUR][1000 genomes]
rs4852305	0.91[CEU][hapmap];0.93[JPT][hapmap];0.94[EUR][1000 genomes]
rs4852308	0.89[ASN][1000 genomes]
rs4852309	0.87[EUR][1000 genomes]
rs4852310	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4852311	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4852936	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4852937	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4852940	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4852948	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4852949	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4852956	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4852958	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4852959	0.92[CHB][hapmap]
rs55677218	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56054150	0.80[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56068325	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56770679	0.94[EUR][1000 genomes]
rs6546830	0.83[EUR][1000 genomes]
rs6546831	0.94[EUR][1000 genomes]
rs6546832	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs6546833	0.87[EUR][1000 genomes]
rs6546834	0.94[EUR][1000 genomes]
rs6546842	0.95[EUR][1000 genomes]
rs6546858	0.83[YRI][hapmap]
rs6546863	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546865	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6546870	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.89[EUR][1000 genomes]
rs66931335	0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6712242	0.87[EUR][1000 genomes]
rs6718799	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6725284	0.89[EUR][1000 genomes]
rs6729347	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6732440	1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs6734450	0.94[EUR][1000 genomes]
rs6742619	0.92[CHB][hapmap];0.88[JPT][hapmap];0.82[YRI][hapmap]
rs6743576	0.88[ASN][1000 genomes]
rs6744273	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6745480	0.83[YRI][hapmap]
rs6745560	0.84[CHB][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs6746458	0.94[EUR][1000 genomes]
rs6749680	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs6759464	0.94[EUR][1000 genomes]
rs67877078	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67898050	0.94[EUR][1000 genomes]
rs68154245	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72811939	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7566315	0.81[ASN][1000 genomes]
rs7570014	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7579068	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7585668	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7598901	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs7607989	0.84[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7608308	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7609034	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7609249	0.88[ASN][1000 genomes]
rs780388	0.94[EUR][1000 genomes]
rs780389	0.94[EUR][1000 genomes]
rs780390	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs780396	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs802113	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
2	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
3	chr2:73765800-73837800	Weak transcription	Fetal Brain Male	brain
4	chr2:73785400-73838200	Weak transcription	Psoas Muscle	Psoas
5	chr2:73792200-73828600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:73797400-73828400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:73800400-73827600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr2:73800600-73828000	Weak transcription	Gastric	stomach
9	chr2:73800600-73828400	Weak transcription	Aorta	Aorta
10	chr2:73800600-73828600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:73800800-73827800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:73800800-73827800	Weak transcription	Left Ventricle	heart
13	chr2:73800800-73828000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:73800800-73828200	Weak transcription	Brain Substantia Nigra	brain
15	chr2:73800800-73828800	Weak transcription	HSMM	muscle
16	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
17	chr2:73807000-73828200	Weak transcription	Fetal Thymus	thymus
18	chr2:73807600-73828000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:73807600-73828000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr2:73807600-73829200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:73807800-73827400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr2:73808200-73827800	Weak transcription	Fetal Stomach	stomach
23	chr2:73808400-73828000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:73808600-73828000	Weak transcription	Thymus	Thymus
25	chr2:73808800-73828000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:73808800-73828000	Weak transcription	Adipose Nuclei	Adipose
27	chr2:73812800-73828600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:73815600-73827400	Weak transcription	Primary T cells from cord blood	blood
29	chr2:73815600-73827600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr2:73815600-73828200	Weak transcription	Fetal Brain Female	brain
31	chr2:73815600-73828200	Weak transcription	HepG2	liver
32	chr2:73815600-73828400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:73815600-73828400	Weak transcription	Brain Anterior Caudate	brain
34	chr2:73815600-73836000	Weak transcription	A549	lung
35	chr2:73815800-73826000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:73815800-73828000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr2:73815800-73828200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:73816000-73827800	Weak transcription	Brain Hippocampus Middle	brain
39	chr2:73816000-73828000	Weak transcription	Brain Angular Gyrus	brain
40	chr2:73816000-73829000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr2:73816400-73827800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr2:73817400-73827800	Weak transcription	Fetal Intestine Large	intestine
43	chr2:73819600-73829400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:73820000-73828000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr2:73820600-73828400	Weak transcription	Spleen	Spleen
46	chr2:73821000-73828400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr2:73821400-73828000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:73821600-73830000	Weak transcription	Osteobl	bone
49	chr2:73821800-73828200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:73821800-73828400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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