Variant report

Variant	rs12204740
Chromosome Location	chr6:133140693-133140694
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:32)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:32 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:133139023..133140882-chr6:133238687..133240373,2	MCF-7	breast:
2	chr6:132935279..132937061-chr6:133139072..133141964,2	K562	blood:
3	chr6:133139865..133142318-chr6:133176855..133179137,2	K562	blood:
4	chr6:133139552..133142163-chr6:133253017..133254972,3	K562	blood:
5	chr6:132832857..132835191-chr6:133139455..133141127,3	K562	blood:
6	chr6:132990956..132993235-chr6:133139715..133142471,3	K562	blood:
7	chr6:133139209..133141849-chr6:133290608..133292386,2	MCF-7	breast:
8	chr6:133140267..133142584-chr6:133384243..133385857,2	MCF-7	breast:
9	chr6:133139056..133141484-chr6:133198427..133200409,2	MCF-7	breast:
10	chr6:133139979..133142138-chr6:133214137..133215920,2	MCF-7	breast:
11	chr6:133140432..133142390-chr6:133219540..133222428,2	MCF-7	breast:
12	chr3:64145733..64148089-chr6:133139687..133142420,2	MCF-7	breast:
13	chr6:133140438..133142973-chr6:133152186..133155729,4	K562	blood:
14	chr11:18417141..18419717-chr6:133139653..133142088,2	K562	blood:
15	chr6:133139807..133142163-chr6:133253017..133254906,2	K562	blood:
16	chr6:132893374..132895125-chr6:133139533..133141338,2	K562	blood:
17	chr19:12885475..12887158-chr6:133138358..133141147,2	K562	blood:
18	chr6:133072472..133075164-chr6:133139801..133141888,2	K562	blood:
19	chr17:41276882..41277419-chr6:133140221..133140863,2	NB4	blood:
20	chr6:132832873..132835191-chr6:133139473..133141127,2	K562	blood:
21	chr6:133139563..133143378-chr6:133869645..133873437,4	K562	blood:
22	chr15:34330929..34333080-chr6:133140289..133142201,2	MCF-7	breast:
23	chr6:133140291..133143900-chr6:133848629..133850657,3	MCF-7	breast:
24	chr6:132849284..132852259-chr6:133140271..133142677,3	MCF-7	breast:
25	chr6:133139428..133141767-chr6:133455373..133456926,2	K562	blood:
26	chr6:133140672..133145394-chr6:133829879..133833202,4	K562	blood:
27	chr6:133140486..133142664-chr6:133322602..133325155,3	K562	blood:
28	chr6:133139605..133142425-chr6:133167716..133170536,3	MCF-7	breast:
29	chr6:133139130..133141825-chr6:133875719..133879392,4	MCF-7	breast:
30	chr6:133139381..133142834-chr6:134271951..134274965,4	K562	blood:
31	chr6:132976419..132978417-chr6:133140501..133142676,2	MCF-7	breast:
32	chr1:149223494..149225494-chr6:133139275..133142169,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction
ENSG00000028839	Chromatin interaction
ENSG00000012048	Chromatin interaction
ENSG00000234484	Chromatin interaction
ENSG00000227954	Chromatin interaction
ENSG00000238059	Chromatin interaction
ENSG00000134333	Chromatin interaction
ENSG00000095066	Chromatin interaction
ENSG00000169857	Chromatin interaction
ENSG00000079950	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10457591	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457593	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457595	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457596	0.85[CEU][hapmap]
rs10484628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11154698	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1128998	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11758796	0.81[ASN][1000 genomes]
rs12190684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12191058	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193474	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12194625	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12194802	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195249	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196336	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197430	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198970	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12199381	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];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12200848	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201540	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201769	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202407	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12203738	0.92[ASN][1000 genomes]
rs12204027	1.00[CHB][hapmap]
rs12204693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207011	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]
rs12209144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12211425	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212934	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215084	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12215088	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12215486	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061751	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2143387	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2294761	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28693848	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706652	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3778173	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]
rs3778175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813347	1.00[JPT][hapmap]
rs55708537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959738	0.85[ASN][1000 genomes]
rs56170227	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58265543	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59543333	0.82[EUR][1000 genomes]
rs60062075	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60412119	0.85[ASN][1000 genomes]
rs62425110	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425113	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425114	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425133	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425137	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62426668	0.81[ASN][1000 genomes]
rs62426674	0.81[ASN][1000 genomes]
rs6934161	1.00[CHB][hapmap]
rs9375919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389032	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9389033	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402452	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402453	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9402455	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9493445	1.00[CHB][hapmap]
rs9493446	1.00[CHB][hapmap]

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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv886676	chr6:133111706-133168582	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	esv1806734	chr6:133125643-133168582	Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12204740	C6orf192	Cis_1M	lymphoblastoid	RTeQTL
rs12204740	C6orf192	cis	lymphoblastoid	seeQTL
rs12204740	C6orf192	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133137200-133145400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:133137400-133141000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:133137400-133141000	Strong transcription	Aorta	Aorta
4	chr6:133137400-133141200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
5	chr6:133137400-133141400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr6:133137600-133141200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr6:133137800-133140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:133137800-133141000	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr6:133137800-133141200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:133137800-133141200	Strong transcription	Placenta	Placenta
11	chr6:133137800-133141400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:133137800-133141400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr6:133137800-133141600	Strong transcription	Fetal Thymus	thymus
14	chr6:133137800-133142200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:133137800-133142400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:133137800-133142400	Strong transcription	Stomach Smooth Muscle	stomach
17	chr6:133137800-133143600	Weak transcription	Right Atrium	heart
18	chr6:133138000-133140800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr6:133138000-133140800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:133138000-133140800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:133138000-133140800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr6:133138000-133140800	Strong transcription	Brain Substantia Nigra	brain
23	chr6:133138000-133141000	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:133138000-133141000	Strong transcription	Brain Anterior Caudate	brain
25	chr6:133138000-133141000	Strong transcription	Rectal Mucosa Donor 31	rectum
26	chr6:133138000-133141000	Strong transcription	Thymus	Thymus
27	chr6:133138000-133141200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:133138000-133141200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:133138000-133141200	Strong transcription	Liver	Liver
30	chr6:133138000-133141200	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr6:133138000-133141200	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:133138000-133141400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:133138000-133141400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr6:133138000-133141400	Strong transcription	Colon Smooth Muscle	Colon
35	chr6:133138000-133141400	Strong transcription	Fetal Intestine Large	intestine
36	chr6:133138000-133141400	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:133138000-133141600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr6:133138000-133141600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr6:133138200-133140800	Strong transcription	Colonic Mucosa	Colon
40	chr6:133138200-133141200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr6:133138200-133141200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:133138200-133141200	Strong transcription	Brain Germinal Matrix	brain
43	chr6:133138200-133141200	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr6:133138200-133141200	Strong transcription	Fetal Lung	lung
45	chr6:133138200-133141200	Strong transcription	Spleen	Spleen
46	chr6:133138400-133140800	Genic enhancers	NHLF	lung
47	chr6:133138400-133141200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:133138400-133141200	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr6:133138400-133141400	Strong transcription	Primary hematopoietic stem cells	blood
50	chr6:133138400-133141400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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