Variant report

Variant	rs12215708
Chromosome Location	chr6:143768106-143768107
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:143768104-143768252	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:143739328..143741392-chr6:143767117..143770115,2	K562	blood:
2	chr6:143767111..143769378-chr6:143810919..143812953,2	MCF-7	breast:
3	chr6:143766653..143768751-chr6:143830885..143833884,2	K562	blood:
4	chr6:143736255..143738473-chr6:143767645..143769544,3	K562	blood:
5	chr6:143766903..143769099-chr6:143857967..143860627,2	MCF-7	breast:
6	chr6:143761031..143767695-chr6:143768053..143772068,9	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP221	TF binding region
ADAT2	TF binding region
PEX3	TF binding region
ENSG00000241847	Chromatin interaction
ENSG00000189007	Chromatin interaction
ENSG00000229036	Chromatin interaction
ENSG00000001036	Chromatin interaction
ENSG00000112419	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1138410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215709	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17072606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432871	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2432872	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2432873	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2473453	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2473454	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496586	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496587	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2496588	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496589	0.89[EUR][1000 genomes]
rs2496591	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496594	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496595	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496597	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748071	1.00[JPT][hapmap]
rs4605902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865962	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336947	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6570561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915676	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915856	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921520	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6921706	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72988621	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72988635	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755370	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761741	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321907	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9321912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9399444	1.00[CHB][hapmap]
rs9484744	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484745	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484746	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484747	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484748	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484750	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484752	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9484753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9496616	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496617	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496618	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496624	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496625	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496627	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496628	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9496629	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496630	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496634	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496637	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496638	0.88[EUR][1000 genomes]
rs9496639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496640	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9496644	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9496649	1.00[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12215708	ADAT2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143733200-143770400	Weak transcription	A549	lung
2	chr6:143742400-143770800	Weak transcription	Spleen	Spleen
3	chr6:143742800-143770200	Weak transcription	Psoas Muscle	Psoas
4	chr6:143744400-143770800	Weak transcription	Left Ventricle	heart
5	chr6:143745800-143770600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:143747400-143770600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:143748000-143770400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr6:143748200-143770600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:143748400-143770400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:143748400-143770600	Weak transcription	Fetal Kidney	kidney
11	chr6:143748400-143770600	Weak transcription	NHDF-Ad	bronchial
12	chr6:143748400-143770600	Weak transcription	NHLF	lung
13	chr6:143749400-143770400	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:143749600-143770800	Weak transcription	Esophagus	oesophagus
15	chr6:143749800-143770400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:143750800-143770200	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:143750800-143770200	Weak transcription	Thymus	Thymus
18	chr6:143751000-143770800	Weak transcription	HSMMtube	muscle
19	chr6:143751600-143770200	Weak transcription	Fetal Intestine Small	intestine
20	chr6:143751600-143770400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:143751600-143770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr6:143752400-143770200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:143752600-143770600	Weak transcription	Brain Substantia Nigra	brain
24	chr6:143753000-143770200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr6:143753800-143770400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr6:143754000-143770200	Weak transcription	Hela-S3	cervix
27	chr6:143754200-143770400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr6:143755200-143770800	Weak transcription	Gastric	stomach
29	chr6:143755200-143770800	Weak transcription	Ovary	ovary
30	chr6:143755400-143770400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:143756000-143770600	Weak transcription	Fetal Brain Female	brain
32	chr6:143757600-143770200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr6:143757800-143771000	Weak transcription	Lung	lung
34	chr6:143758000-143770200	Weak transcription	Pancreas	Pancrea
35	chr6:143758000-143770400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:143758000-143770400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr6:143758000-143770800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr6:143758200-143770600	Weak transcription	Brain Anterior Caudate	brain
39	chr6:143759800-143770400	Weak transcription	HSMM	muscle
40	chr6:143760000-143769800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr6:143760000-143769800	Weak transcription	HMEC	breast
42	chr6:143760000-143770200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr6:143760000-143770200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr6:143760000-143770200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:143760000-143770200	Weak transcription	Fetal Thymus	thymus
46	chr6:143760000-143770200	Weak transcription	HUVEC	blood vessel
47	chr6:143760000-143770400	Weak transcription	Liver	Liver
48	chr6:143760000-143770400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:143760000-143770600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:143760200-143770200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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