Variant report

Variant	rs34400564
Chromosome Location	chr1:227361253-227361254
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227361245..227362795-chr1:227368024..227369819,2	K562	blood:
2	chr1:227360994..227362712-chr1:227365141..227367307,2	K562	blood:
3	chr1:227360407..227362745-chr1:227368024..227370354,2	K562	blood:

Variant related genes	Relation type
ENSG00000228625	Chromatin interaction

Extended variants
information (count: 182 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:177)

rs_ID	r²[population]
rs1015815	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1015816	0.88[EUR][1000 genomes]
rs10495258	0.82[EUR][1000 genomes]
rs10495263	0.81[EUR][1000 genomes]
rs10495266	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10495269	0.82[EUR][1000 genomes]
rs10495270	0.82[EUR][1000 genomes]
rs10916109	0.94[EUR][1000 genomes]
rs10916114	0.92[EUR][1000 genomes]
rs11799413	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11800062	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11801443	0.81[EUR][1000 genomes]
rs11801994	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11802395	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11803590	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11803761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803959	0.81[EUR][1000 genomes]
rs11805298	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11806511	0.89[EUR][1000 genomes]
rs11806820	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11806937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808186	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11808928	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11809998	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11810328	0.92[EUR][1000 genomes]
rs11811358	0.91[EUR][1000 genomes]
rs12401963	0.82[EUR][1000 genomes]
rs12402456	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12403195	0.82[EUR][1000 genomes]
rs12403391	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12403650	0.93[EUR][1000 genomes]
rs12403833	0.82[EUR][1000 genomes]
rs12403986	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12404494	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12404627	0.82[EUR][1000 genomes]
rs12405122	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12405363	0.90[EUR][1000 genomes]
rs12405686	0.82[EUR][1000 genomes]
rs12405878	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12407061	0.82[EUR][1000 genomes]
rs12407545	0.82[EUR][1000 genomes]
rs12408437	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12408913	0.93[EUR][1000 genomes]
rs12409816	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12410327	0.90[EUR][1000 genomes]
rs12410337	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12410460	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12411017	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12741049	0.84[EUR][1000 genomes]
rs1320493	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1464076	0.90[EUR][1000 genomes]
rs1464077	0.92[EUR][1000 genomes]
rs1513600	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1513602	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1513603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1546557	0.92[EUR][1000 genomes]
rs1606549	0.92[EUR][1000 genomes]
rs16846855	0.82[EUR][1000 genomes]
rs16846874	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16846877	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16846908	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16846910	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16846911	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16846972	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16846985	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847014	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847035	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847098	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16847492	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16847634	0.90[EUR][1000 genomes]
rs17605533	0.82[EUR][1000 genomes]
rs17613166	0.93[EUR][1000 genomes]
rs17851754	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1877622	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1888831	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2090009	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2150871	0.82[EUR][1000 genomes]
rs2150873	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2183837	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34263105	0.90[EUR][1000 genomes]
rs34953255	0.82[EUR][1000 genomes]
rs41270149	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4255349	0.88[EUR][1000 genomes]
rs4282782	0.92[EUR][1000 genomes]
rs4300186	0.90[EUR][1000 genomes]
rs4354510	0.90[EUR][1000 genomes]
rs4434814	0.92[EUR][1000 genomes]
rs4437846	0.91[EUR][1000 genomes]
rs4518864	0.92[EUR][1000 genomes]
rs4543764	0.83[EUR][1000 genomes]
rs4551563	0.82[EUR][1000 genomes]
rs55685166	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55805110	0.92[EUR][1000 genomes]
rs55865118	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55882852	0.91[EUR][1000 genomes]
rs55946024	0.93[EUR][1000 genomes]
rs56834719	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57276421	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57513303	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57758974	0.92[EUR][1000 genomes]
rs58489467	0.94[EUR][1000 genomes]
rs58532064	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59116340	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59121440	0.92[EUR][1000 genomes]
rs59859849	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60068245	0.92[EUR][1000 genomes]
rs60079575	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60235610	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60291100	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60641481	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60742095	0.91[EUR][1000 genomes]
rs60866629	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60958272	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60979561	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61081394	0.92[EUR][1000 genomes]
rs61522132	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6659506	0.92[EUR][1000 genomes]
rs6668367	0.87[EUR][1000 genomes]
rs6675383	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs6696791	0.83[EUR][1000 genomes]
rs6696794	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6701743	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73086746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73086752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73086775	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73088658	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089725	0.82[EUR][1000 genomes]
rs73089747	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73089755	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73089760	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73089765	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73089770	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73090612	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091738	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091740	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091742	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091755	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091759	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091761	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091774	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73093463	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73093495	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73094351	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73094393	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73094400	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73096317	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73096350	0.94[EUR][1000 genomes]
rs73096353	0.94[EUR][1000 genomes]
rs73096358	0.92[EUR][1000 genomes]
rs73096374	0.91[EUR][1000 genomes]
rs73098390	0.90[EUR][1000 genomes]
rs73098398	0.90[EUR][1000 genomes]
rs73099023	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73099026	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73100804	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73100814	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73100852	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73102307	0.85[EUR][1000 genomes]
rs73102915	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73102920	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73102930	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73102936	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7413768	0.84[EUR][1000 genomes]
rs74140153	0.92[EUR][1000 genomes]
rs74140276	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs74143321	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7515739	0.92[EUR][1000 genomes]
rs7519099	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7526283	0.91[EUR][1000 genomes]
rs7534286	0.98[EUR][1000 genomes]
rs7535010	0.98[EUR][1000 genomes]
rs7539037	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7539750	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7542505	0.91[EUR][1000 genomes]
rs7544923	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7545775	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7551556	0.92[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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227317000-227374200	Weak transcription	HepG2	liver
4	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
5	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:227343200-227400400	Weak transcription	A549	lung
9	chr1:227346800-227366600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
14	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:227347800-227363600	Weak transcription	Fetal Stomach	stomach
16	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:227348200-227367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr1:227348200-227370200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:227348200-227370400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:227348200-227371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:227348200-227376400	Weak transcription	Fetal Lung	lung
23	chr1:227348200-227377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:227348200-227377800	Weak transcription	HUVEC	blood vessel
25	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:227348400-227378000	Weak transcription	Liver	Liver
32	chr1:227354800-227374400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr1:227355000-227374800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:227356800-227361400	Enhancers	Fetal Heart	heart
37	chr1:227357600-227374400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:227358600-227362400	Weak transcription	Right Atrium	heart
39	chr1:227358600-227374000	Weak transcription	Left Ventricle	heart
40	chr1:227358800-227361600	Enhancers	K562	blood
41	chr1:227358800-227374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:227359400-227374000	Weak transcription	Pancreas	Pancrea
44	chr1:227359400-227374400	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
46	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
47	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
49	chr1:227360000-227361400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:227360800-227363600	Enhancers	HSMM	muscle

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