Variant report

Variant	rs6553777
Chromosome Location	chr4:175190159-175190160
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:175181041..175183420-chr4:175187913..175190511,2	MCF-7	breast:
2	chr4:175184412..175187975-chr4:175189059..175193975,5	K562	blood:
3	chr4:175190016..175192606-chr4:175201922..175204827,4	K562	blood:
4	chr4:175189453..175192652-chr4:175201823..175204827,4	K562	blood:

Variant related genes	Relation type
ENSG00000164117	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10034021	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs10520275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10565	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11933187	0.80[YRI][hapmap]
rs11939946	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11944262	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11946084	0.89[CEU][hapmap]
rs13101580	0.80[YRI][hapmap]
rs13128257	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130276	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13150997	0.80[EUR][1000 genomes]
rs1508222	0.86[ASN][1000 genomes]
rs17291087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291128	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17291408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17357120	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs1995749	0.80[EUR][1000 genomes]
rs2332836	0.82[CEU][hapmap]
rs41279509	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4695915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695922	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs68084371	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6851312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702217	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7661236	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6553777	CEP44	cis	Thyroid	GTEx
rs6553777	KIAA1712	cis	multi-tissue	Pritchard

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175147600-175195200	Weak transcription	Psoas Muscle	Psoas
2	chr4:175151400-175192800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr4:175153400-175191600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:175154200-175204000	Weak transcription	Aorta	Aorta
5	chr4:175154200-175204200	Weak transcription	Esophagus	oesophagus
6	chr4:175154400-175202400	Weak transcription	Gastric	stomach
7	chr4:175158800-175202000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:175159800-175199800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:175161000-175192400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:175169800-175203600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr4:175171800-175195200	Weak transcription	Pancreas	Pancrea
12	chr4:175174800-175199800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:175174800-175203400	Weak transcription	Thymus	Thymus
14	chr4:175175000-175196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:175175000-175198600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:175177400-175190400	Weak transcription	Fetal Kidney	kidney
17	chr4:175177400-175197800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:175177600-175192000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:175178000-175198600	Weak transcription	K562	blood
20	chr4:175178000-175203600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:175178200-175191400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:175178200-175193800	Weak transcription	HSMMtube	muscle
23	chr4:175179200-175192200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr4:175179200-175204000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr4:175179400-175202400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:175181000-175201600	Weak transcription	Fetal Thymus	thymus
27	chr4:175181600-175196200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr4:175181600-175203400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:175181600-175203600	Weak transcription	Primary hematopoietic stem cells	blood
30	chr4:175182200-175202600	Weak transcription	Fetal Intestine Small	intestine
31	chr4:175184000-175195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr4:175184200-175193600	Weak transcription	Lung	lung
33	chr4:175184200-175197800	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr4:175184200-175199800	Weak transcription	Dnd41	blood
35	chr4:175184200-175202400	Weak transcription	Fetal Intestine Large	intestine
36	chr4:175184200-175203600	Weak transcription	HSMM	muscle
37	chr4:175184400-175190400	Weak transcription	Adipose Nuclei	Adipose
38	chr4:175184400-175200800	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr4:175184400-175202400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr4:175184400-175202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:175184400-175204000	Weak transcription	Left Ventricle	heart
42	chr4:175184800-175191200	Weak transcription	Ovary	ovary
43	chr4:175184800-175202400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr4:175187400-175198600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr4:175187600-175198600	Weak transcription	Fetal Brain Female	brain
46	chr4:175187800-175198600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr4:175187800-175202200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:175188000-175195200	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:175188000-175198200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:175188200-175198600	Weak transcription	GM12878-XiMat	blood

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