Variant report

Variant	rs28663544
Chromosome Location	chr4:174138867-174138868
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:174134446..174136321-chr4:174137572..174139819,3	MCF-7	breast:
2	chr4:174137352..174140088-chr4:174184722..174187553,2	K562	blood:
3	chr4:174138653..174140508-chr4:174254407..174256256,2	K562	blood:
4	chr4:174134665..174137165-chr4:174138818..174141532,2	K562	blood:
5	chr4:174120841..174123019-chr4:174137354..174139118,2	K562	blood:
6	chr4:174138498..174140984-chr4:174142749..174145611,3	K562	blood:

Variant related genes	Relation type
ENSG00000164104	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10001613	0.95[EUR][1000 genomes]
rs1008052	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10213525	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11731263	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112928	0.86[EUR][1000 genomes]
rs17059221	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2332655	0.83[EUR][1000 genomes]
rs28377337	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28451250	0.86[ASN][1000 genomes]
rs28477861	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28769285	0.81[AMR][1000 genomes]
rs4535319	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60815517	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6817013	0.87[ASN][1000 genomes]
rs72711045	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683937	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9685946	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9999740	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1799519	chr4:174090004-174173743	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv518900	chr4:174130503-174142874	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:174104000-174157200	Weak transcription	Ovary	ovary
2	chr4:174112800-174140000	Weak transcription	Aorta	Aorta
3	chr4:174114200-174157800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:174114600-174155000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr4:174123600-174174200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr4:174125600-174144800	Weak transcription	Primary B cells from cord blood	blood
7	chr4:174125800-174139200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:174126000-174156400	Weak transcription	Brain Anterior Caudate	brain
9	chr4:174126400-174149800	Weak transcription	Esophagus	oesophagus
10	chr4:174126600-174155200	Weak transcription	GM12878-XiMat	blood
11	chr4:174126600-174163400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr4:174126800-174139000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr4:174127000-174139600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:174127000-174148600	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr4:174127000-174163600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:174127000-174163600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:174127400-174149000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:174128200-174139000	Weak transcription	Primary T cells from cord blood	blood
19	chr4:174128200-174169200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr4:174130200-174139400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:174131000-174139000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr4:174131200-174147800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:174131800-174140200	Weak transcription	Thymus	Thymus
24	chr4:174131800-174156400	Weak transcription	Fetal Intestine Small	intestine
25	chr4:174131800-174168600	Weak transcription	Gastric	stomach
26	chr4:174132800-174150600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:174133000-174139000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:174135800-174146800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:174136000-174139600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr4:174136200-174139600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:174136600-174158400	Weak transcription	Fetal Muscle Leg	muscle
32	chr4:174136800-174139600	Weak transcription	Fetal Thymus	thymus
33	chr4:174136800-174157200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:174137200-174143200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:174138200-174139800	Enhancers	Stomach Mucosa	stomach
36	chr4:174138200-174140000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:174138200-174140400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr4:174138200-174140400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:174138200-174140400	Enhancers	NHEK	skin
40	chr4:174138200-174140600	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr4:174138200-174140600	Enhancers	Dnd41	blood
42	chr4:174138400-174139000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:174138400-174139000	Enhancers	Muscle Satellite Cultured Cells	--
44	chr4:174138400-174139400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:174138400-174139600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:174138400-174139600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr4:174138400-174139800	Flanking Active TSS	A549	lung
48	chr4:174138400-174140000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:174138400-174140400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:174138400-174140400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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