Variant report

Variant	rs6657728
Chromosome Location	chr1:212255695-212255696
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	chr1:212255227..212257947-chr1:212264882..212267056,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10779568	0.87[ASN][1000 genomes]
rs10863936	0.82[JPT][hapmap]
rs10863939	0.87[ASN][1000 genomes]
rs11119836	0.82[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs11119839	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119840	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119843	0.85[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs12070369	0.87[YRI][hapmap]
rs12076757	0.82[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs1316820	0.81[ASN][1000 genomes]
rs1578992	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1578993	0.84[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs1806360	0.87[ASN][1000 genomes]
rs1933593	0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2014029	0.86[JPT][hapmap]
rs2105162	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2130503	0.99[ASN][1000 genomes]
rs2248191	0.86[JPT][hapmap]
rs2251398	0.87[ASN][1000 genomes]
rs2358386	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2358440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2788139	0.81[JPT][hapmap]
rs2788140	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs2808392	0.90[JPT][hapmap]
rs2884428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2884457	0.87[ASN][1000 genomes]
rs2970592	0.97[ASN][1000 genomes]
rs2970599	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2970601	0.90[JPT][hapmap]
rs2993529	0.86[ASN][1000 genomes]
rs2993531	0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap]
rs2993533	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2993544	0.90[JPT][hapmap]
rs3010003	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs3010004	0.81[JPT][hapmap]
rs3010023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3010024	0.90[ASN][1000 genomes]
rs3738449	0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs4093392	0.83[AFR][1000 genomes]
rs4951435	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4951561	0.81[LWK][hapmap];0.87[YRI][hapmap]
rs4951567	0.82[JPT][hapmap];0.87[YRI][hapmap]
rs55806741	0.83[AFR][1000 genomes]
rs61828539	0.83[AFR][1000 genomes]
rs61828547	0.83[AFR][1000 genomes]
rs6684814	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66858610	0.81[AFR][1000 genomes]
rs67417805	0.81[AFR][1000 genomes]
rs7522330	0.88[ASN][1000 genomes]
rs7540968	0.82[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes]
rs7550754	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6657728	INTS7	Cis_1M	lymphoblastoid	RTeQTL
rs6657728	PROX1	cis	cerebellum	SCAN
rs6657728	C1orf74	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212214400-212278000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:212229600-212266600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:212229800-212255800	Weak transcription	Thymus	Thymus
4	chr1:212229800-212261000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:212229800-212261200	Weak transcription	Fetal Stomach	stomach
6	chr1:212229800-212261400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:212229800-212263000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:212229800-212266400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:212230000-212261200	Weak transcription	Osteobl	bone
10	chr1:212230000-212265200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:212230800-212261800	Weak transcription	Primary B cells from cord blood	blood
12	chr1:212231400-212261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:212233000-212266400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:212234000-212265400	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:212234000-212265800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:212234200-212267400	Strong transcription	Dnd41	blood
17	chr1:212236000-212265200	Strong transcription	K562	blood
18	chr1:212237000-212261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:212237000-212266200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr1:212237200-212267000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:212237600-212260800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:212237600-212266800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:212237800-212262000	Strong transcription	Hela-S3	cervix
24	chr1:212238200-212261200	Weak transcription	NH-A	brain
25	chr1:212241600-212264200	Weak transcription	Fetal Brain Female	brain
26	chr1:212241600-212284600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:212242000-212261200	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:212244600-212267200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:212247200-212261400	Weak transcription	Fetal Kidney	kidney
30	chr1:212248200-212261600	Weak transcription	Psoas Muscle	Psoas
31	chr1:212249400-212266000	Strong transcription	A549	lung
32	chr1:212249800-212257200	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr1:212250200-212259600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:212250200-212260000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:212250800-212257400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:212251200-212257200	Strong transcription	HMEC	breast
37	chr1:212251400-212255800	Strong transcription	HUVEC	blood vessel
38	chr1:212251400-212257200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:212251400-212257400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:212251600-212261200	Weak transcription	Gastric	stomach
41	chr1:212251800-212259000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:212252200-212258000	Weak transcription	Brain Germinal Matrix	brain
43	chr1:212252200-212261000	Strong transcription	Fetal Thymus	thymus
44	chr1:212252400-212259600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:212253000-212270800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:212253200-212256000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr1:212253200-212256400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:212253200-212257600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr1:212253200-212259400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr1:212253400-212256400	Strong transcription	HepG2	liver

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