Variant report

Variant	rs885912
Chromosome Location	chr6:30174633-30174634
allele	G/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	HNF4G	chr6:30174526-30175451	HepG2	liver:	n/a	chr6:30175273-30175288 chr6:30174972-30174987
2	FOXA2	chr6:30174418-30175442	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30174570-30175609	HepG2	liver:	n/a	n/a
4	HNF4A	chr6:30174553-30175461	HepG2	liver:	n/a	chr6:30175273-30175288 chr6:30174978-30174993
5	HEY1	chr6:30174537-30175508	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:30174329-30175926	HepG2	liver:	n/a	n/a
7	MYBL2	chr6:30174205-30176177	HepG2	liver:	n/a	n/a
8	TBP	chr6:30174631-30175666	HepG2	liver:	n/a	chr6:30175407-30175418
9	STAT3	chr6:30174380-30175066	MCF10A-Er-Src	breast:	n/a	chr6:30174785-30174797
10	MAX	chr6:30174368-30175889	HepG2	liver:	n/a	chr6:30175301-30175310 chr6:30175303-30175310
11	FOXA1	chr6:30174362-30175506	HepG2	liver:	n/a	n/a
12	SP1	chr6:30174505-30175280	A549	lung:	n/a	n/a
13	MBD4	chr6:30174591-30176006	HepG2	liver:	n/a	n/a
14	POLR2A	chr6:30174564-30176036	HepG2	liver:	n/a	n/a
15	NFIC	chr6:30174482-30175671	HepG2	liver:	n/a	n/a
16	MYC	chr6:30174533-30175490	MCF10A-Er-Src	breast:	n/a	chr6:30175301-30175310 chr6:30175303-30175310
17	HNF4G	chr6:30174592-30175505	HepG2	liver:	n/a	chr6:30175273-30175288 chr6:30174972-30174987
18	POLR2A	chr6:30174570-30175561	HepG2	liver:	n/a	n/a
19	MYC	chr6:30174609-30175097	HepG2	liver:	n/a	n/a
20	MAX	chr6:30174584-30175155	A549	lung:	n/a	n/a
21	MYC	chr6:30174440-30175581	MCF10A-Er-Src	breast:	n/a	chr6:30175301-30175310 chr6:30175303-30175310
22	MAX	chr6:30174589-30175594	HepG2	liver:	n/a	chr6:30175301-30175310 chr6:30175303-30175310
23	TEAD4	chr6:30174628-30175212	ECC-1	luminal epithelium:	n/a	n/a
24	HDAC2	chr6:30174487-30175432	HepG2	liver:	n/a	chr6:30175393-30175407
25	POLR2A	chr6:30174571-30176242	GM12878	blood:	n/a	n/a
26	ARID3A	chr6:30174614-30175421	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:30174632-30174921	HepG2	liver:	n/a	n/a
28	EP300	chr6:30174513-30175637	ECC-1	luminal epithelium:	n/a	n/a
29	TEAD4	chr6:30174443-30175539	HepG2	liver:	n/a	n/a
30	MYBL2	chr6:30174466-30175577	HepG2	liver:	n/a	n/a
31	BHLHE40	chr6:30174563-30175537	HepG2	liver:	n/a	n/a
32	FOXA1	chr6:30174310-30175509	HepG2	liver:	n/a	n/a
33	SP1	chr6:30174450-30175765	HepG2	liver:	n/a	n/a
34	HNF4A	chr6:30174581-30175394	HepG2	liver:	n/a	chr6:30175273-30175288 chr6:30174978-30174993
35	TCF12	chr6:30174584-30175397	ECC-1	luminal epithelium:	n/a	n/a
36	HDAC2	chr6:30174570-30175477	HepG2	liver:	n/a	chr6:30175393-30175407
37	MBD4	chr6:30174603-30175487	HepG2	liver:	n/a	n/a
38	EP300	chr6:30174618-30175375	HepG2	liver:	n/a	n/a
39	MAX	chr6:30174460-30175866	HepG2	liver:	n/a	chr6:30175301-30175310 chr6:30175303-30175310
40	NR3C1	chr6:30174537-30174812	A549	lung:	n/a	n/a
41	POLR2A	chr6:30174435-30175829	GM12878	blood:	n/a	n/a
42	FOXA1	chr6:30174328-30175465	HepG2	liver:	n/a	n/a
43	FOXA2	chr6:30174483-30175183	A549	lung:	n/a	n/a
44	MXI1	chr6:30174600-30175612	HepG2	liver:	n/a	n/a
45	POLR2A	chr6:30174561-30175640	HepG2	liver:	n/a	n/a
46	REST	chr6:30174586-30175552	HepG2	liver:	n/a	chr6:30174683-30174696
47	FOXA2	chr6:30174446-30174989	A549	lung:	n/a	n/a
48	FOXA1	chr6:30174420-30175517	HepG2	liver:	n/a	n/a
49	EP300	chr6:30174536-30175657	HepG2	liver:	n/a	n/a
50	HEY1	chr6:30174475-30175686	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30112108..30113874-chr6:30174193..30176985,2	K562	blood:
2	chr6:30170611..30172995-chr6:30173743..30176690,2	MCF-7	breast:
3	chr6:30172695..30175243-chr6:30183856..30185988,2	K562	blood:

Variant related genes	Relation type
TRIM26	TF binding region
ENSG00000234127	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1117487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1117488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1117490	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11969573	0.81[ASN][1000 genomes]
rs2021722	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023475	0.81[ASN][1000 genomes]
rs2284166	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428503	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2517590	0.81[ASN][1000 genomes]
rs2517608	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517610	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517611	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2517614	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2523713	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523716	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2523721	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2523722	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28360014	0.81[ASN][1000 genomes]
rs2844776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3132672	0.81[AFR][1000 genomes]
rs55957413	0.81[ASN][1000 genomes]
rs59975149	0.81[ASN][1000 genomes]
rs61154150	0.81[ASN][1000 genomes]
rs971570	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs885912	ZKSCAN3	cis	parietal	SCAN
rs885912	BTN2A1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30150600-30179200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:30158400-30179600	Weak transcription	Fetal Brain Male	brain
3	chr6:30167000-30178000	Weak transcription	Fetal Brain Female	brain
4	chr6:30168800-30174800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:30168800-30179800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:30169000-30174800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:30169000-30175000	Weak transcription	Ovary	ovary
8	chr6:30169000-30175000	Weak transcription	HUVEC	blood vessel
9	chr6:30169000-30175200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:30169000-30175400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:30169000-30179800	Weak transcription	Aorta	Aorta
12	chr6:30169400-30175200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:30170200-30175000	Strong transcription	Fetal Stomach	stomach
14	chr6:30170200-30179200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr6:30170400-30175000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:30170600-30174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr6:30170600-30179600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:30171600-30176200	Strong transcription	Primary T cells from cord blood	blood
19	chr6:30172000-30174800	Genic enhancers	Fetal Intestine Small	intestine
20	chr6:30172000-30176000	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr6:30172200-30174800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:30172400-30174800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr6:30172400-30174800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:30172400-30175000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:30172400-30175200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:30172400-30179200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr6:30172600-30176800	Weak transcription	Dnd41	blood
28	chr6:30172600-30178400	Enhancers	Esophagus	oesophagus
29	chr6:30172600-30179800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:30172800-30175200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:30173000-30175600	Enhancers	Lung	lung
32	chr6:30173000-30176200	Genic enhancers	Primary T cells fromperipheralblood	blood
33	chr6:30173000-30176200	Enhancers	Fetal Heart	heart
34	chr6:30173000-30177200	Strong transcription	Thymus	Thymus
35	chr6:30173000-30179200	Genic enhancers	Primary B cells from peripheral blood	blood
36	chr6:30173200-30176000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:30173200-30178400	Enhancers	Pancreas	Pancrea
38	chr6:30173400-30174800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:30173400-30175200	Weak transcription	Brain Germinal Matrix	brain
40	chr6:30173400-30176000	Enhancers	Gastric	stomach
41	chr6:30173400-30176200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:30173400-30176200	Enhancers	Left Ventricle	heart
43	chr6:30173400-30179600	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr6:30173400-30179800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:30173400-30179800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr6:30173600-30175200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:30173600-30175800	Enhancers	Fetal Muscle Trunk	muscle
48	chr6:30173600-30176200	Enhancers	Psoas Muscle	Psoas
49	chr6:30173600-30176600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:30173800-30175000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--

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