Variant report

Variant	rs3132582
Chromosome Location	chr6:30689001-30689002
allele	A/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	BCL11A	chr6:30688893-30689346	GM12878	blood:	n/a	n/a
2	SPI1	chr6:30688919-30689425	HL-60	blood:	n/a	chr6:30689151-30689164
3	CREB1	chr6:30688865-30689427	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr6:30688848-30689506	SK-N-SH	brain:	n/a	n/a
5	MAX	chr6:30687465-30689845	HCT-116	colon:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
6	TCF7L2	chr6:30688994-30689629	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr6:30687422-30690021	H1-neurons	neurons:	n/a	n/a
8	TEAD4	chr6:30688904-30689551	ECC-1	luminal epithelium:	n/a	n/a
9	GABPA	chr6:30688995-30689661	K562	blood:	n/a	chr6:30689310-30689319 chr6:30689346-30689360 chr6:30689349-30689363 chr6:30689349-30689360
10	BCLAF1	chr6:30686890-30689854	GM12878	blood:	n/a	chr6:30689371-30689384 chr6:30688101-30688110
11	TAF1	chr6:30688897-30689268	PFSK-1	brain:	n/a	n/a
12	POLR2A	chr6:30687736-30689679	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr6:30687742-30694690	GM12878	blood:	n/a	n/a
14	CHD1	chr6:30687430-30689809	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr6:30688947-30689724	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr6:30687413-30689987	HCT-116	colon:	n/a	n/a
17	MAX	chr6:30688514-30689580	H1-hESC	embryonic stem cell:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
18	CREB1	chr6:30688556-30689658	HepG2	liver:	n/a	n/a
19	TBL1XR1	chr6:30687159-30689445	K562	blood:	n/a	n/a
20	POLR2A	chr6:30688887-30689336	MCF10A-Er-Src	breast:	n/a	n/a
21	CBX3	chr6:30688499-30689617	K562	blood:	n/a	n/a
22	EGR1	chr6:30688965-30689671	MCF-7	breast:	n/a	chr6:30689375-30689385 chr6:30689310-30689325 chr6:30689371-30689381 chr6:30689308-30689322 chr6:30689312-30689322 chr6:30689311-30689324 chr6:30689350-30689359 chr6:30689155-30689164 chr6:30689311-30689324 chr6:30689312-30689323 chr6:30689138-30689151 chr6:30689312-30689321 chr6:30689309-30689319 chr6:30689311-30689324 chr6:30689311-30689324 chr6:30689310-30689324 chr6:30689312-30689322
23	MAX	chr6:30687507-30689656	K562	blood:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
24	POLR2A	chr6:30687036-30695449	HUVEC	blood vessel:	n/a	n/a
25	ARID3A	chr6:30688820-30689614	HepG2	liver:	n/a	n/a
26	EGR1	chr6:30688969-30689611	K562	blood:	n/a	chr6:30689375-30689385 chr6:30689310-30689325 chr6:30689371-30689381 chr6:30689308-30689322 chr6:30689312-30689322 chr6:30689311-30689324 chr6:30689350-30689359 chr6:30689155-30689164 chr6:30689311-30689324 chr6:30689312-30689323 chr6:30689138-30689151 chr6:30689312-30689321 chr6:30689309-30689319 chr6:30689311-30689324 chr6:30689311-30689324 chr6:30689310-30689324 chr6:30689312-30689322
27	JUND	chr6:30688945-30689702	MCF-7	breast:	n/a	chr6:30689375-30689384 chr6:30689376-30689385
28	JUND	chr6:30688962-30690029	A549	lung:	n/a	chr6:30689375-30689384 chr6:30689376-30689385
29	REST	chr6:30686831-30691010	H1-neurons	neurons:	n/a	chr6:30690432-30690445 chr6:30688079-30688092
30	SP1	chr6:30688930-30689546	GM12878	blood:	n/a	chr6:30689309-30689319 chr6:30689275-30689284 chr6:30689371-30689383 chr6:30689275-30689284 chr6:30689368-30689382 chr6:30689308-30689320 chr6:30689276-30689285 chr6:30689143-30689153 chr6:30689309-30689319 chr6:30689184-30689195 chr6:30689275-30689289 chr6:30689274-30689286 chr6:30689142-30689153 chr6:30689372-30689381 chr6:30689143-30689152 chr6:30689275-30689285 chr6:30689309-30689318 chr6:30689308-30689320 chr6:30689144-30689158 chr6:30689147-30689159 chr6:30689371-30689383 chr6:30689274-30689286 chr6:30689142-30689154 chr6:30689199-30689210 chr6:30689310-30689319 chr6:30689144-30689153 chr6:30689142-30689154 chr6:30689275-30689285
31	POLR2A	chr6:30687122-30694167	H1-hESC	embryonic stem cell:	n/a	n/a
32	BCL3	chr6:30688974-30689548	GM12878	blood:	n/a	chr6:30689371-30689384
33	POLR2A	chr6:30683610-30695318	SK-N-MC	brain:	n/a	n/a
34	TAF1	chr6:30687749-30689559	GM12878	blood:	n/a	n/a
35	BCL3	chr6:30687929-30689292	A549	lung:	n/a	chr6:30688101-30688110
36	CHD1	chr6:30687056-30690038	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr6:30688831-30689325	GM12878	blood:	n/a	n/a
38	POLR2A	chr6:30688594-30689681	HepG2	liver:	n/a	n/a
39	SP1	chr6:30688901-30689323	GM12878	blood:	n/a	chr6:30689309-30689319 chr6:30689275-30689284 chr6:30689275-30689284 chr6:30689308-30689320 chr6:30689276-30689285 chr6:30689143-30689153 chr6:30689309-30689319 chr6:30689184-30689195 chr6:30689275-30689289 chr6:30689274-30689286 chr6:30689142-30689153 chr6:30689143-30689152 chr6:30689275-30689285 chr6:30689309-30689318 chr6:30689308-30689320 chr6:30689144-30689158 chr6:30689147-30689159 chr6:30689274-30689286 chr6:30689142-30689154 chr6:30689199-30689210 chr6:30689310-30689319 chr6:30689144-30689153 chr6:30689142-30689154 chr6:30689275-30689285
40	REST	chr6:30688979-30689516	SK-N-SH	brain:	n/a	n/a
41	STAT5A	chr6:30687974-30689487	GM12878	blood:	n/a	chr6:30688745-30688757
42	GATA3	chr6:30688990-30689682	MCF-7	breast:	n/a	n/a
43	ZBTB7A	chr6:30688960-30689487	HepG2	liver:	n/a	n/a
44	MAX	chr6:30687495-30689914	A549	lung:	n/a	chr6:30689309-30689319 chr6:30689372-30689382 chr6:30689313-30689322
45	ELF1	chr6:30688969-30689453	A549	lung:	n/a	n/a
46	PML	chr6:30686897-30691157	GM12878	blood:	n/a	chr6:30687409-30687417
47	POLR2A	chr6:30687365-30689684	K562	blood:	n/a	n/a
48	BHLHE40	chr6:30688921-30689712	GM12878	blood:	n/a	n/a
49	TAF1	chr6:30687558-30689469	ECC-1	luminal epithelium:	n/a	n/a
50	CREB1	chr6:30688875-30689378	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30687338..30691474-chr6:30850428..30854318,11	MCF-7	breast:
2	chr6:30629679..30632498-chr6:30687159..30689670,2	MCF-7	breast:
3	chr6:30455560..30457980-chr6:30688126..30690528,2	K562	blood:
4	chr6:30613134..30616889-chr6:30684889..30690956,7	MCF-7	breast:
5	chr1:11967863..11968473-chr6:30688369..30689328,2	Hela-S3	cervix:
6	chr22:31365932..31368594-chr6:30687396..30689377,2	K562	blood:
7	chr6:30688404..30690517-chr6:30855397..30858284,2	MCF-7	breast:
8	chr6:30687707..30689680-chr6:30855398..30858038,2	MCF-7	breast:
9	chr6:30522151..30525852-chr6:30686505..30691954,11	K562	blood:
10	chr6:30576582..30588788-chr6:30682721..30700088,114	K562	blood:
11	chr1:23885712..23886483-chr6:30688984..30689705,2	Hela-S3	cervix:
12	chr6:30634661..30668428-chr6:30680318..30698953,145	MCF-7	breast:
13	chr6:30608315..30616989-chr6:30683761..30694958,31	K562	blood:
14	chr6:30591444..30595401-chr6:30685466..30689259,5	K562	blood:
15	chr6:30688042..30689988-chr8:145577489..145580277,2	MCF-7	breast:
16	chr6:30687770..30690244-chr6:30875447..30877174,2	MCF-7	breast:
17	chr15:60689912..60690621-chr6:30688405..30689136,2	Hela-S3	cervix:
18	chr1:43478758..43479258-chr6:30688143..30689094,2	NB4	blood:
19	chr6:30638422..30642374-chr6:30687329..30691225,7	MCF-7	breast:
20	chr11:64884386..64886553-chr6:30687642..30689654,2	MCF-7	breast:
21	chr6:30538999..30540963-chr6:30688916..30690569,2	MCF-7	breast:
22	chr6:30577862..30587208-chr6:30682997..30696247,43	MCF-7	breast:
23	chr6:30522474..30526619-chr6:30688958..30690909,4	MCF-7	breast:
24	chr1:45988000..45988805-chr6:30688919..30689665,2	Hela-S3	cervix:
25	chr3:101568696..101569256-chr6:30688635..30689565,2	Hela-S3	cervix:
26	chr6:30688767..30689308-chr7:106624610..106625110,2	HCT-116	colon:
27	chr6:30687753..30689397-chr6:36409717..36412070,2	K562	blood:
28	chr6:30685105..30690458-chr6:30847596..30854595,13	MCF-7	breast:
29	chr6:30590782..30598373-chr6:30685661..30690473,13	MCF-7	breast:
30	chr6:30515029..30517945-chr6:30687848..30689600,2	MCF-7	breast:
31	chr6:30522706..30525361-chr6:30686394..30690570,5	MCF-7	breast:
32	chr6:30455790..30458568-chr6:30687436..30691942,4	MCF-7	breast:
33	chr6:30643326..30660432-chr6:30681522..30696111,127	MCF-7	breast:
34	chr6:30688723..30690650-chr6:30849267..30850908,2	K562	blood:
35	chr20:30192762..30193415-chr6:30689001..30689722,2	Hela-S3	cervix:
36	chr6:30577773..30589670-chr6:30680333..30700280,58	MCF-7	breast:

Variant related genes	Relation type
MDC1	TF binding region
TUBB	TF binding region
ENSG00000204592	Chromatin interaction
ENSG00000112078	Chromatin interaction
ENSG00000266183	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000204564	Chromatin interaction
ENSG00000182718	Chromatin interaction
ENSG00000204574	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000185803	Chromatin interaction
ENSG00000214597	Chromatin interaction
ENSG00000204560	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000204569	Chromatin interaction
ENSG00000144802	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000117318	Chromatin interaction
ENSG00000137343	Chromatin interaction
ENSG00000125968	Chromatin interaction
ENSG00000204576	Chromatin interaction
ENSG00000179165	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000253352	Chromatin interaction
ENSG00000204590	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000230449	Chromatin interaction
ENSG00000146112	Chromatin interaction
ENSG00000271698	Chromatin interaction
ENSG00000213780	Chromatin interaction
ENSG00000137404	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000117450	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1059612	0.91[EUR][1000 genomes]
rs3094125	0.92[EUR][1000 genomes]
rs3095326	0.81[EUR][1000 genomes]
rs3095327	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3095328	0.82[EUR][1000 genomes]
rs3095332	0.82[EUR][1000 genomes]
rs3129972	0.83[EUR][1000 genomes]
rs3129973	0.81[EUR][1000 genomes]
rs3129974	0.82[EUR][1000 genomes]
rs3130658	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130660	0.92[EUR][1000 genomes]
rs3132583	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132585	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3132600	0.81[EUR][1000 genomes]
rs9262126	0.88[EUR][1000 genomes]
rs9262130	0.88[EUR][1000 genomes]
rs9262132	0.88[EUR][1000 genomes]
rs9262135	0.88[EUR][1000 genomes]
rs9262141	0.85[EUR][1000 genomes]
rs9262142	0.85[EUR][1000 genomes]
rs9262143	0.85[EUR][1000 genomes]
rs9262146	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3132582	TUBB	Cis_1M	lymphoblastoid	RTeQTL
rs3132582	HLA-C	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30684400-30690200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30684800-30689600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:30685200-30689400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:30686600-30689400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:30686600-30689400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:30687000-30689400	Active TSS	H1 Cell Line	embryonic stem cell
7	chr6:30687000-30689400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:30687000-30689600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:30687000-30689600	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr6:30687000-30690200	Active TSS	GM12878-XiMat	blood
11	chr6:30687000-30690400	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr6:30687200-30689200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:30687200-30689400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:30687200-30689400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:30687200-30689400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:30687200-30689400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr6:30687200-30689400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:30687200-30689400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:30687200-30689400	Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr6:30687200-30689400	Active TSS	K562	blood
21	chr6:30687200-30689400	Active TSS	NHLF	lung
22	chr6:30687200-30689600	Active TSS	Fetal Intestine Large	intestine
23	chr6:30687200-30689800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:30687200-30690000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr6:30687200-30690000	Active TSS	Aorta	Aorta
26	chr6:30687200-30690200	Active TSS	Lung	lung
27	chr6:30687200-30690200	Active TSS	HSMMtube	muscle
28	chr6:30687200-30690400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:30687200-30690800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr6:30687400-30689400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:30687400-30689400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr6:30687400-30689400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:30687400-30689400	Active TSS	Fetal Lung	lung
34	chr6:30687400-30689400	Active TSS	Fetal Stomach	stomach
35	chr6:30687400-30689400	Active TSS	Pancreas	Pancrea
36	chr6:30687400-30689400	Active TSS	A549	lung
37	chr6:30687400-30689600	Active TSS	Stomach Mucosa	stomach
38	chr6:30687400-30689800	Active TSS	Brain Substantia Nigra	brain
39	chr6:30687400-30689800	Active TSS	Spleen	Spleen
40	chr6:30687400-30689800	Active TSS	NHDF-Ad	bronchial
41	chr6:30687400-30690000	Active TSS	Ovary	ovary
42	chr6:30687400-30690000	Active TSS	Sigmoid Colon	Sigmoid Colon
43	chr6:30687400-30690200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:30687400-30690200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:30687400-30690200	Active TSS	Esophagus	oesophagus
46	chr6:30687400-30690400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:30687400-30690400	Active TSS	Placenta Amnion	Placenta Amnion
48	chr6:30687400-30690400	Active TSS	Right Ventricle	heart
49	chr6:30687600-30689400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:30687600-30689400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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