Variant report

Variant	rs12647034
Chromosome Location	chr4:56310622-56310623
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	chr4:56309719..56312179-chr4:56315380..56317885,2	K562	blood:
2	chr4:56309987..56312642-chr4:56314579..56316616,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134852	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10002541	0.84[EUR][1000 genomes]
rs10005989	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10016506	0.84[EUR][1000 genomes]
rs10462035	0.86[EUR][1000 genomes]
rs11133379	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133382	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11133383	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11133399	0.81[EUR][1000 genomes]
rs11726609	0.84[EUR][1000 genomes]
rs11733864	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11735267	0.87[EUR][1000 genomes]
rs11931061	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11939815	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11947476	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11947623	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12646078	0.85[EUR][1000 genomes]
rs13102385	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13121235	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13128582	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13138697	0.87[EUR][1000 genomes]
rs13152650	0.87[EUR][1000 genomes]
rs1522106	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1522107	0.85[EUR][1000 genomes]
rs1522108	0.86[EUR][1000 genomes]
rs1522110	0.86[EUR][1000 genomes]
rs1522111	0.88[EUR][1000 genomes]
rs17085889	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1965467	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1980273	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2140077	0.87[EUR][1000 genomes]
rs2177129	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2412646	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2412647	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28525309	0.81[EUR][1000 genomes]
rs28582059	0.81[EUR][1000 genomes]
rs28670674	0.82[EUR][1000 genomes]
rs28790098	0.84[EUR][1000 genomes]
rs35767091	0.87[EUR][1000 genomes]
rs3736544	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3736545	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805147	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3805152	0.86[EUR][1000 genomes]
rs3805154	0.87[EUR][1000 genomes]
rs3805157	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3817444	0.86[EUR][1000 genomes]
rs3828481	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4371676	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4580704	0.88[EUR][1000 genomes]
rs473005	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs480479	0.81[EUR][1000 genomes]
rs4864998	0.87[EUR][1000 genomes]
rs4865008	0.82[EUR][1000 genomes]
rs564762	0.81[EUR][1000 genomes]
rs576779	0.81[EUR][1000 genomes]
rs62303714	0.88[EUR][1000 genomes]
rs62309727	0.83[EUR][1000 genomes]
rs6554286	0.83[EUR][1000 genomes]
rs6810948	0.82[EUR][1000 genomes]
rs6811520	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6812042	0.84[EUR][1000 genomes]
rs6815516	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6817267	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6819660	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6824057	0.85[EUR][1000 genomes]
rs6824955	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6825994	0.81[EUR][1000 genomes]
rs6832769	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6834676	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6837710	0.86[EUR][1000 genomes]
rs6839788	0.81[EUR][1000 genomes]
rs6846427	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6853192	0.80[EUR][1000 genomes]
rs7667849	0.85[EUR][1000 genomes]
rs7668147	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7670225	0.85[EUR][1000 genomes]
rs7673908	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7677526	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7684810	0.87[EUR][1000 genomes]
rs9312662	0.86[EUR][1000 genomes]
rs9997288	0.87[EUR][1000 genomes]
rs9998038	0.84[EUR][1000 genomes]
rs9998146	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328582	chr4:56164136-56486156	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
2	nsv999477	chr4:56219035-56397180	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv537101	chr4:56219035-56397180	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv1011722	chr4:56261349-56325600	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56265600-56319800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:56268800-56326000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:56269000-56311400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr4:56274600-56332200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr4:56276000-56320000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:56279000-56321800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56280800-56311000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:56288400-56318400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:56290800-56340400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr4:56290800-56340600	Weak transcription	Thymus	Thymus
11	chr4:56293000-56324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:56293000-56354800	Weak transcription	Aorta	Aorta
13	chr4:56294000-56311400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr4:56294000-56341200	Weak transcription	Small Intestine	intestine
15	chr4:56296200-56314600	Weak transcription	Psoas Muscle	Psoas
16	chr4:56296200-56314600	Weak transcription	Hela-S3	cervix
17	chr4:56299600-56311400	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr4:56301600-56310800	Weak transcription	Ovary	ovary
19	chr4:56301600-56334800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr4:56301800-56313200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr4:56301800-56314000	Weak transcription	A549	lung
22	chr4:56301800-56314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr4:56301800-56316200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr4:56301800-56316200	Weak transcription	Rectal Smooth Muscle	rectum
25	chr4:56301800-56318000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr4:56301800-56318000	Weak transcription	Right Ventricle	heart
27	chr4:56301800-56332200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:56301800-56339200	Weak transcription	Fetal Brain Male	brain
29	chr4:56302000-56314000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr4:56302200-56312600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr4:56302200-56313200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr4:56302200-56313400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr4:56302200-56313600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr4:56302200-56314000	Weak transcription	Fetal Heart	heart
35	chr4:56302200-56314400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr4:56302200-56314800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:56302200-56315600	Weak transcription	Fetal Stomach	stomach
38	chr4:56302400-56375600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:56302600-56311600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:56303000-56311400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr4:56303000-56340200	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:56303200-56311200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr4:56303600-56314200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr4:56304000-56331800	Weak transcription	Esophagus	oesophagus
45	chr4:56304600-56316200	Weak transcription	Lung	lung
46	chr4:56304600-56365600	Weak transcription	Spleen	Spleen
47	chr4:56304800-56311400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr4:56304800-56311400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:56304800-56314000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:56304800-56314600	Weak transcription	Colonic Mucosa	Colon

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