Variant report

Variant	rs12185567
Chromosome Location	chr2:172560729-172560730
allele	A/C
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	CTCF	chr2:172560580-172560730	GM06990	blood:	n/a	n/a
2	RAD21	chr2:172559858-172560943	SK-N-SH	brain:	n/a	chr2:172560308-172560327
3	CTCF	chr2:172559944-172560938	A549	lung:	n/a	chr2:172560308-172560324 chr2:172560309-172560330 chr2:172560307-172560325
4	CTCF	chr2:172560660-172560810	AG09319	gingival:	n/a	n/a
5	CTCF	chr2:172559936-172560754	SK-N-SH	brain:	n/a	chr2:172560308-172560324 chr2:172560309-172560330 chr2:172560307-172560325
6	CTCF	chr2:172560580-172560730	NHDF-neo	bronchial:	n/a	n/a
7	SMC3	chr2:172559871-172560986	SK-N-SH	brain:	n/a	chr2:172560309-172560323

No.	Distal block	Cell Line	Cell type
1	chr2:172559872..172560770-chr2:173574898..173575445,2	K562	blood:
2	chr2:172557694..172560489-chr2:172560501..172562511,2	K562	blood:
3	chr2:172430340..172431211-chr2:172559859..172560852,2	MCF-7	breast:
4	chr2:172429933..172431336-chr2:172560125..172561039,3	K562	blood:
5	chr2:172560229..172560733-chr2:172991740..172992317,2	MCF-7	breast:
6	chr2:172558563..172561388-chr2:172862907..172864950,2	K562	blood:
7	chr2:172560231..172560811-chr2:172978149..172978700,2	K562	blood:
8	chr2:172558785..172561244-chr2:172563256..172565056,2	K562	blood:
9	chr2:172560578..172564258-chr2:172967186..172970481,4	K562	blood:
10	chr2:172559867..172560730-chr2:172968303..172969236,3	K562	blood:
11	chr2:172454934..172455567-chr2:172559837..172560822,3	MCF-7	breast:
12	chr2:172559888..172562408-chr2:172862907..172864805,2	K562	blood:
13	chr2:172558785..172561475-chr2:172562570..172565056,4	K562	blood:

Variant related genes	Relation type
DYNC1I2	TF binding region
ENSG00000115844	Chromatin interaction
ENSG00000077380	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000236651	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10166005	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10167419	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10174525	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10184866	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10194102	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10200608	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10201419	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204502	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10204622	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10206062	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10207085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497374	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10803863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1113389	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11678984	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11692132	0.85[YRI][hapmap]
rs11757	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11886820	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11897196	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11904009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12053003	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12692970	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12692973	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12692974	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12692978	0.87[CEU][hapmap];0.86[CHB][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13017585	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13018768	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13022113	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13419987	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13429113	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13429409	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474074	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1554166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1973706	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2357061	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2674484	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2678155	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs312916	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs312919	0.94[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs312921	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs312924	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs312925	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34358700	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34542126	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35379278	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35391289	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35549875	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35854280	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36057702	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770445	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770451	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3770452	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3795999	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667693	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4668407	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4668412	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4668414	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433311	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433314	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66835971	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6705200	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6709156	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6710698	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67204065	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6721680	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6722757	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6724337	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6725388	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs6738445	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6745143	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6754817	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6757773	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6758704	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6759575	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71013062	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7355523	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7355594	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7562356	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7572215	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7573003	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs7586207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7597387	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7604918	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7608403	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs908670	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs908671	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs973889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12185567	AC068039.4	cis	Esophagus Muscularis	GTEx
rs12185567	AC068039.4	cis	Whole Blood	GTEx
rs12185567	AC068039.4	cis	Muscle Skeletal	GTEx
rs12185567	AC068039.4	cis	Esophagus Mucosa	GTEx
rs12185567	AC068039.4	cis	Heart Left Ventricle	GTEx
rs12185567	AC068039.4	cis	lung	GTEx
rs12185567	AC068039.4	cis	Thyroid	GTEx
rs12185567	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs12185567	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs12185567	AC068039.4	cis	Nerve Tibial	GTEx
rs12185567	AC068039.4	cis	Stomach	GTEx
rs12185567	AC068039.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172545000-172580200	Weak transcription	Pancreas	Pancrea
2	chr2:172545000-172580400	Weak transcription	Spleen	Spleen
3	chr2:172545000-172580800	Weak transcription	Gastric	stomach
4	chr2:172545200-172611200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:172545400-172588000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr2:172545800-172573000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:172545800-172575400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr2:172545800-172588000	Weak transcription	Right Ventricle	heart
9	chr2:172546000-172563000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:172546000-172567800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:172546000-172568600	Weak transcription	Hela-S3	cervix
12	chr2:172546400-172561200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:172546400-172574600	Weak transcription	Right Atrium	heart
14	chr2:172546600-172602800	Weak transcription	Small Intestine	intestine
15	chr2:172547000-172578600	Weak transcription	Fetal Brain Male	brain
16	chr2:172547200-172561000	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:172548200-172571800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr2:172548400-172579600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:172550200-172564200	Weak transcription	HMEC	breast
20	chr2:172550200-172567800	Weak transcription	Dnd41	blood
21	chr2:172551600-172584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:172552200-172573400	Weak transcription	Fetal Brain Female	brain
23	chr2:172552200-172587600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:172554000-172580200	Weak transcription	Aorta	Aorta
25	chr2:172554400-172563800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:172554400-172566200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:172554400-172588000	Weak transcription	Esophagus	oesophagus
28	chr2:172554600-172572000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:172554600-172572200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:172554800-172562600	Weak transcription	A549	lung
31	chr2:172554800-172564400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:172554800-172580400	Weak transcription	K562	blood
33	chr2:172555000-172564400	Weak transcription	Placenta	Placenta
34	chr2:172555000-172566400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:172555000-172571800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:172555000-172571800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:172555000-172580200	Weak transcription	Brain Anterior Caudate	brain
38	chr2:172555200-172562800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr2:172555200-172563600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:172555600-172566400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:172556000-172561200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:172556400-172560800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:172556400-172561600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:172556800-172568600	Weak transcription	Fetal Kidney	kidney
45	chr2:172557000-172563800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:172557000-172566200	Weak transcription	Left Ventricle	heart
47	chr2:172557000-172568600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:172557000-172571800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:172557200-172563000	Weak transcription	NHEK	skin
50	chr2:172557200-172564200	Weak transcription	NH-A	brain

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