Variant report

Variant	rs1768671
Chromosome Location	chr1:220164915-220164916
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr1:220164695-220165723	PBDE	blood:	n/a	n/a
2	CTCF	chr1:220164258-220164970	HCT-116	colon:	n/a	chr1:220164526-220164547 chr1:220164529-220164537 chr1:220164524-220164542
3	CTCF	chr1:220164043-220165084	SK-N-SH	brain:	n/a	chr1:220164526-220164547 chr1:220164529-220164537 chr1:220164524-220164542
4	CTCF	chr1:220164104-220165175	A549	lung:	n/a	chr1:220164526-220164547 chr1:220164529-220164537 chr1:220164524-220164542
5	POLR2A	chr1:220161313-220168073	K562	blood:	n/a	n/a
6	RAD21	chr1:220164166-220165365	SK-N-SH	brain:	n/a	chr1:220164527-220164534 chr1:220164525-220164544
7	ZNF384	chr1:220164311-220164976	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:220153591..220159773-chr1:220159981..220165102,9	K562	blood:
2	chr1:220164810..220167759-chr1:220168424..220170636,2	K562	blood:
3	chr1:220164112..220164967-chr1:220297177..220297836,2	MCF-7	breast:
4	chr1:220163102..220165191-chr1:220201695..220204471,2	K562	blood:
5	chr1:220049633..220050383-chr1:220164327..220165162,2	MCF-7	breast:
6	chr1:220144163..220148221-chr1:220163054..220166012,3	K562	blood:
7	chr1:220163484..220165362-chr1:220165481..220167153,2	K562	blood:
8	chr1:220163115..220165079-chr1:220292412..220294107,2	K562	blood:
9	chr1:220072242..220074837-chr1:220162775..220165302,2	K562	blood:
10	chr1:220011035..220013766-chr1:220162762..220165197,2	K562	blood:

Variant related genes	Relation type
ENSG00000238798	TF binding region
ENSG00000136628	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10442684	0.84[EUR][1000 genomes]
rs10746395	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10746396	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10779395	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10779396	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12140664	0.89[CEU][hapmap]
rs12141971	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12142009	0.91[EUR][1000 genomes]
rs1566252	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1611961	0.96[EUR][1000 genomes]
rs1612144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1614384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1614585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1614719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1622508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1658226	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1658227	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1694576	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1694577	0.84[CEU][hapmap]
rs1694599	0.85[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs1694600	0.87[EUR][1000 genomes]
rs1768665	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1768666	0.88[CEU][hapmap]
rs1768667	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1768669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1768673	0.88[CEU][hapmap]
rs1768674	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1768676	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1768677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1874810	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2230301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2245457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2248466	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2248479	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2248717	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2248719	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577138	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2577140	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577141	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577142	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577144	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577145	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577146	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2577148	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577149	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577150	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577151	0.93[EUR][1000 genomes]
rs2577156	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577158	0.85[EUR][1000 genomes]
rs2577159	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577160	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2577163	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2577165	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2647420	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647422	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647423	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647424	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647426	0.86[EUR][1000 genomes]
rs2647427	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2647428	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647429	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647430	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647432	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2647433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647434	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2647438	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2647441	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2647445	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647446	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647447	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647448	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647449	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647452	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647454	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647457	0.88[EUR][1000 genomes]
rs2647462	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2647467	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2647469	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2647470	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2647478	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2647479	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789793	0.87[EUR][1000 genomes]
rs2789794	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789797	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2789800	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789802	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789803	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2789806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2789807	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2789809	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2789811	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2789812	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789813	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789815	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789816	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789817	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2789819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2795310	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2795314	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2795315	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6541120	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6681055	0.83[EUR][1000 genomes]
rs6681471	0.92[EUR][1000 genomes]
rs6681474	0.95[EUR][1000 genomes]
rs6703042	0.90[EUR][1000 genomes]
rs7537058	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7545314	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7548397	0.95[EUR][1000 genomes]
rs7550249	0.83[AMR][1000 genomes];0.96[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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	738 gene(s)	inside rSNPs	diseases
4	esv1798515	chr1:220157811-220167371	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220132800-220177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220140000-220167400	Weak transcription	Gastric	stomach
3	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
6	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:220142600-220169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:220146400-220182800	Weak transcription	Spleen	Spleen
9	chr1:220147200-220169400	Weak transcription	Fetal Heart	heart
10	chr1:220149000-220167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:220149400-220178200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:220149600-220166800	Weak transcription	Stomach Mucosa	stomach
13	chr1:220153600-220169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr1:220154200-220169200	Weak transcription	Fetal Brain Male	brain
15	chr1:220154400-220169200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:220154400-220169200	Weak transcription	Fetal Lung	lung
17	chr1:220154600-220166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:220154600-220167000	Weak transcription	Aorta	Aorta
19	chr1:220154600-220169000	Weak transcription	Small Intestine	intestine
20	chr1:220154600-220169200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr1:220154800-220167400	Weak transcription	Pancreas	Pancrea
22	chr1:220155000-220166000	Weak transcription	Brain Germinal Matrix	brain
23	chr1:220155600-220168600	Weak transcription	Brain Substantia Nigra	brain
24	chr1:220156800-220169800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr1:220157000-220168800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:220157200-220167000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:220157200-220177200	Weak transcription	Esophagus	oesophagus
28	chr1:220158200-220166000	Weak transcription	Lung	lung
29	chr1:220158200-220167200	Weak transcription	Ovary	ovary
30	chr1:220158200-220177200	Weak transcription	Right Ventricle	heart
31	chr1:220159200-220166200	Weak transcription	Fetal Stomach	stomach
32	chr1:220159200-220168800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:220159800-220169200	Weak transcription	Colonic Mucosa	Colon
34	chr1:220160200-220168600	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:220160400-220167400	Weak transcription	Primary B cells from cord blood	blood
36	chr1:220160400-220168600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:220160600-220167000	Enhancers	Liver	Liver
38	chr1:220160800-220166000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:220160800-220169200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:220160800-220174200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:220161000-220165400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:220161000-220167400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr1:220161000-220168800	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:220161000-220168800	Weak transcription	Thymus	Thymus
45	chr1:220161000-220169200	Weak transcription	Psoas Muscle	Psoas
46	chr1:220161000-220169200	Weak transcription	NHLF	lung
47	chr1:220161200-220166600	Weak transcription	Fetal Brain Female	brain
48	chr1:220161200-220168800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:220161200-220169200	Weak transcription	Left Ventricle	heart
50	chr1:220161600-220168800	Weak transcription	Primary hematopoietic stem cells	blood

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