Variant report

Variant	rs6427261
Chromosome Location	chr1:170519337-170519338
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:170511995..170514709-chr1:170517192..170519375,2	MCF-7	breast:
2	chr1:170519224..170521087-chr1:170524845..170527316,2	MCF-7	breast:
3	chr1:170498743..170500327-chr1:170518394..170520763,2	K562	blood:

Variant related genes	Relation type
ENSG00000120370	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10733056	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10753814	0.91[AFR][1000 genomes]
rs10753815	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs10800527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10919425	0.88[AFR][1000 genomes]
rs10919429	1.00[AMR][1000 genomes]
rs12068399	1.00[AMR][1000 genomes]
rs12116909	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333133	0.92[ASW][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs1333142	1.00[YRI][hapmap]
rs1333150	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1333155	0.90[AFR][1000 genomes]
rs1333156	0.90[AFR][1000 genomes]
rs1412892	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1412895	0.90[AFR][1000 genomes]
rs1537390	1.00[YRI][hapmap]
rs1537395	0.84[YRI][hapmap]
rs1537397	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs1576979	0.89[AFR][1000 genomes]
rs1576980	0.88[AFR][1000 genomes]
rs16863435	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs1855221	0.90[AFR][1000 genomes]
rs1928716	1.00[YRI][hapmap]
rs1930632	0.85[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs2104918	0.87[AFR][1000 genomes]
rs2150029	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes]
rs2225322	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs2421325	1.00[ASW][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2901401	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs3980839	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4233350	0.82[AFR][1000 genomes]
rs4325194	0.94[AFR][1000 genomes]
rs4402174	0.90[AFR][1000 genomes]
rs4415629	0.94[AFR][1000 genomes]
rs4656769	0.85[AFR][1000 genomes]
rs4656775	0.92[AFR][1000 genomes]
rs4656777	0.92[AFR][1000 genomes]
rs4656779	0.83[ASW][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes]
rs4656783	0.97[AFR][1000 genomes]
rs6427260	1.00[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6657164	0.90[AFR][1000 genomes]
rs6660575	0.89[AFR][1000 genomes]
rs6664037	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6667304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6669308	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6670724	0.88[AFR][1000 genomes]
rs6671312	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6676081	0.95[AFR][1000 genomes]
rs6693763	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6699057	0.85[AFR][1000 genomes]
rs6701218	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6703801	0.82[AFR][1000 genomes]
rs7523665	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7531125	0.92[ASW][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs7538125	0.90[AFR][1000 genomes]
rs7548443	0.90[AFR][1000 genomes]
rs7553254	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][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	nsv872543	chr1:170171083-170674903	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv533915	chr1:170258766-170725296	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170502200-170521000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:170502600-170520800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:170502600-170523400	Weak transcription	Fetal Brain Male	brain
4	chr1:170503000-170523600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:170505000-170524800	Strong transcription	Dnd41	blood
6	chr1:170505400-170522800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:170506000-170522200	Strong transcription	Primary B cells from cord blood	blood
8	chr1:170507600-170523600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr1:170507600-170524000	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:170507800-170521800	Strong transcription	Fetal Lung	lung
11	chr1:170507800-170522200	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr1:170507800-170522600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:170508000-170522000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:170508000-170523000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:170508200-170522200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:170508200-170523400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr1:170508200-170524400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:170508400-170519600	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:170508400-170521600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:170508400-170522000	Strong transcription	Placenta	Placenta
21	chr1:170508400-170522200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:170508400-170522200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr1:170508400-170522200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr1:170508400-170522200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:170508400-170522200	Strong transcription	Fetal Thymus	thymus
26	chr1:170508400-170522200	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr1:170508400-170522400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:170508400-170523600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:170508400-170523600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:170508400-170523800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr1:170508400-170523800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:170508800-170524000	Strong transcription	Liver	Liver
33	chr1:170509200-170522200	Strong transcription	Primary T cells from cord blood	blood
34	chr1:170509600-170522200	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr1:170509800-170523600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr1:170512000-170522200	Strong transcription	A549	lung
37	chr1:170512600-170519400	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr1:170512600-170527200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:170512800-170521200	Weak transcription	Colon Smooth Muscle	Colon
40	chr1:170513000-170520800	Weak transcription	Fetal Kidney	kidney
41	chr1:170513200-170520600	Weak transcription	HepG2	liver
42	chr1:170513400-170522000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:170513600-170522000	Strong transcription	Fetal Intestine Large	intestine
44	chr1:170513600-170522000	Strong transcription	Fetal Muscle Leg	muscle
45	chr1:170514000-170532000	Weak transcription	Brain Angular Gyrus	brain
46	chr1:170514200-170520600	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:170514200-170524000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:170514400-170520200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr1:170514400-170526800	Weak transcription	Psoas Muscle	Psoas
50	chr1:170514400-170532000	Weak transcription	Small Intestine	intestine

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