Variant report

Variant	rs6137910
Chromosome Location	chr20:23346515-23346516
allele	C/G
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	POLR2A	chr20:23345662-23352219	GM12878	blood:	n/a	n/a
2	POLR2A	chr20:23346105-23346562	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr20:23346032-23347034	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr20:23341279-23355011	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:23345834-23346779	HepG2	liver:	n/a	n/a
6	POLR2A	chr20:23341069-23355530	K562	blood:	n/a	n/a
7	POLR2A	chr20:23340935-23347328	IMR90	lung:	n/a	n/a
8	CTCF	chr20:23346500-23346650	Caco-2	colon:	n/a	chr20:23346608-23346617 chr20:23346588-23346597
9	CTCF	chr20:23346480-23346630	GM12878	blood:	n/a	chr20:23346608-23346617 chr20:23346588-23346597
10	POLR2A	chr20:23345812-23346836	GM12878	blood:	n/a	n/a
11	POLR2A	chr20:23346314-23348823	GM12891	blood:	n/a	n/a
12	FOSL2	chr20:23346000-23346971	HepG2	liver:	n/a	n/a
13	POLR2A	chr20:23345736-23346937	K562	blood:	n/a	n/a
14	CTCF	chr20:23346500-23346650	GM12864	blood:	n/a	chr20:23346608-23346617 chr20:23346588-23346597
15	POLR2A	chr20:23345454-23347365	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr20:23346421-23346778	H1-hESC	embryonic stem cell:	n/a	chr20:23346491-23346500

No.	Distal block	Cell Line	Cell type
1	chr20:23344681..23346860-chr20:23360081..23363046,2	MCF-7	breast:
2	chr20:23345633..23349899-chr20:23400647..23404181,5	K562	blood:
3	chr20:23345633..23349899-chr20:23400854..23404181,4	K562	blood:

Variant related genes	Relation type
GZF1	TF binding region
ENSG00000125814	Chromatin interaction
ENSG00000201728	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1076776	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12625160	0.85[JPT][hapmap]
rs12625164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12625999	0.89[JPT][hapmap]
rs12626013	0.85[JPT][hapmap]
rs17757228	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]
rs17757442	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17830281	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]
rs1936011	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2277765	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2281428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281434	1.00[CEU][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2295238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34648279	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3736755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3746733	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]
rs3746737	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3761274	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3761275	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3827085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3827086	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55851398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56094936	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56334525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6036423	0.81[JPT][hapmap]
rs6036424	0.84[JPT][hapmap]
rs6048803	0.89[JPT][hapmap]
rs6106669	0.84[JPT][hapmap]
rs6114094	0.89[JPT][hapmap]
rs6114142	0.84[JPT][hapmap]
rs6114144	0.84[JPT][hapmap]
rs6132599	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132600	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6132605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6132606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6132609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6132610	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132617	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6132621	0.85[JPT][hapmap]
rs6132622	0.85[JPT][hapmap]
rs6132623	0.85[JPT][hapmap]
rs6132631	0.81[JPT][hapmap]
rs6137901	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6137907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6137913	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];0.98[ASN][1000 genomes]
rs6137914	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6137915	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];0.98[ASN][1000 genomes]
rs6137917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6137919	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6137927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6137936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137937	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6137938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6137941	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6137945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137947	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137948	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137950	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6137951	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6137957	0.85[JPT][hapmap]
rs6137959	0.85[JPT][hapmap]
rs6137961	0.85[JPT][hapmap]
rs6137975	0.84[JPT][hapmap]
rs761722	0.87[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8183135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6137910	NXT1	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23342400-23352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr20:23344000-23347600	Enhancers	Primary T cells fromperipheralblood	blood
3	chr20:23344000-23392600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:23344200-23346600	Genic enhancers	Spleen	Spleen
5	chr20:23344400-23346600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:23344400-23346600	Strong transcription	Brain Angular Gyrus	brain
7	chr20:23344400-23346600	Weak transcription	Psoas Muscle	Psoas
8	chr20:23344400-23346600	Weak transcription	Hela-S3	cervix
9	chr20:23344400-23347200	Genic enhancers	Dnd41	blood
10	chr20:23344400-23347800	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr20:23344400-23349200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr20:23344400-23350200	Weak transcription	Fetal Kidney	kidney
13	chr20:23344600-23346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr20:23344600-23347000	Enhancers	Fetal Heart	heart
15	chr20:23344600-23354200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:23344800-23346600	Weak transcription	Stomach Mucosa	stomach
17	chr20:23344800-23346600	Strong transcription	NHEK	skin
18	chr20:23344800-23347800	Genic enhancers	Brain Inferior Temporal Lobe	brain
19	chr20:23344800-23347800	Strong transcription	A549	lung
20	chr20:23344800-23348800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
21	chr20:23344800-23362400	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr20:23345000-23346600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr20:23345000-23346600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr20:23345000-23346600	Strong transcription	Fetal Brain Female	brain
25	chr20:23345000-23346600	Strong transcription	Fetal Intestine Small	intestine
26	chr20:23345000-23346600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr20:23345000-23346600	Genic enhancers	Right Ventricle	heart
28	chr20:23345000-23346600	Strong transcription	Thymus	Thymus
29	chr20:23345000-23346800	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr20:23345000-23346800	Strong transcription	Fetal Intestine Large	intestine
31	chr20:23345000-23346800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr20:23345000-23346800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
33	chr20:23345000-23346800	Strong transcription	Osteobl	bone
34	chr20:23345000-23347000	Genic enhancers	Left Ventricle	heart
35	chr20:23345000-23348200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr20:23345000-23349600	Genic enhancers	HepG2	liver
37	chr20:23345000-23361800	Strong transcription	Fetal Thymus	thymus
38	chr20:23345000-23362000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr20:23345000-23362600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr20:23345200-23346600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr20:23345200-23346600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:23345200-23346800	Strong transcription	NHLF	lung
43	chr20:23345200-23347000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr20:23345200-23348200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr20:23345400-23346600	Genic enhancers	Pancreas	Pancrea
46	chr20:23345400-23346800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr20:23345400-23347200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr20:23345400-23347600	Strong transcription	HSMMtube	muscle
49	chr20:23345600-23346600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
50	chr20:23345600-23347200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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