Variant report

Variant	rs3132522
Chromosome Location	chr6:31137759-31137760
allele	A/G
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	SIN3AK20	chr6:31136874-31138073	MCF-7	breast:	n/a	n/a
2	SIN3AK20	chr6:31137718-31138045	H1-hESC	embryonic stem cell:	n/a	n/a
3	TAF1	chr6:31137665-31138615	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr6:31137588-31138643	A549	lung:	n/a	n/a
5	NR2F2	chr6:31137027-31137871	MCF-7	breast:	n/a	n/a
6	TCF12	chr6:31137017-31138015	MCF-7	breast:	n/a	chr6:31137808-31137818
7	HDAC2	chr6:31137056-31137876	MCF-7	breast:	n/a	n/a
8	POLR2A	chr6:31137705-31138667	H1-hESC	embryonic stem cell:	n/a	n/a
9	TFAP2A	chr6:31137123-31137884	Hela-S3	cervix:	n/a	chr6:31137526-31137540 chr6:31137369-31137379 chr6:31137526-31137540 chr6:31137542-31137557 chr6:31137528-31137538 chr6:31137369-31137379 chr6:31137526-31137541 chr6:31137368-31137379 chr6:31137369-31137379 chr6:31137528-31137538 chr6:31137367-31137381 chr6:31137526-31137540
10	GATA3	chr6:31137135-31137867	MCF-7	breast:	n/a	chr6:31137567-31137579
11	GATA3	chr6:31136818-31138007	MCF-7	breast:	n/a	chr6:31137930-31137939 chr6:31137567-31137579
12	HDAC2	chr6:31137219-31137789	MCF-7	breast:	n/a	n/a
13	POLR2A	chr6:31137529-31137848	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3A	chr6:31136616-31138063	H1-hESC	embryonic stem cell:	n/a	chr6:31137868-31137881
15	POLR2A	chr6:31136367-31139334	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr6:31137585-31138268	A549	lung:	n/a	n/a
17	GATA3	chr6:31136918-31138055	MCF-7	breast:	n/a	chr6:31137930-31137939 chr6:31137567-31137579
18	NR2F2	chr6:31136980-31138083	MCF-7	breast:	n/a	n/a
19	POLR2A	chr6:31137329-31138144	H1-hESC	embryonic stem cell:	n/a	n/a
20	SIN3AK20	chr6:31137066-31137924	MCF-7	breast:	n/a	n/a
21	EP300	chr6:31137264-31137783	MCF-7	breast:	n/a	n/a
22	TCF12	chr6:31137074-31137773	MCF-7	breast:	n/a	n/a
23	TFAP2C	chr6:31137093-31137872	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr6:31136889-31137835	HepG2	liver:	n/a	n/a
25	POLR2A	chr6:31137736-31138030	ECC-1	luminal epithelium:	n/a	n/a
26	POLR2A	chr6:31137684-31138055	A549	lung:	n/a	n/a
27	MAX	chr6:31137157-31137991	MCF-7	breast:	n/a	n/a
28	POLR2A	chr6:31137680-31137993	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:31127915..31129464-chr6:31137096..31138939,2	K562	blood:
2	chr6:31129733..31135466-chr6:31137398..31140077,6	K562	blood:
3	chr6:31126958..31132315-chr6:31135299..31140140,6	K562	blood:
4	chr6:31124835..31127745-chr6:31135310..31138711,4	MCF-7	breast:
5	chr6:31137173..31139829-chr6:31146846..31149399,2	MCF-7	breast:
6	chr6:31136072..31138764-chr6:31142991..31146892,3	MCF-7	breast:
7	chr6:31137284..31139502-chr6:31369827..31372777,2	K562	blood:

Variant related genes	Relation type
POU5F1	TF binding region
ENSG00000204536	Chromatin interaction
ENSG00000137310	Chromatin interaction
ENSG00000199332	Chromatin interaction
ENSG00000204528	Chromatin interaction
ENSG00000204531	Chromatin interaction
ENSG00000204520	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1061118	0.82[ASN][1000 genomes]
rs1065461	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs130078	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2022084	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2073719	0.95[EUR][1000 genomes]
rs2073721	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073722	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2073723	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106074	0.83[ASN][1000 genomes]
rs2240059	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2394882	0.82[ASN][1000 genomes]
rs3094192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094194	0.88[ASN][1000 genomes]
rs3094226	0.95[EUR][1000 genomes]
rs3094227	0.82[AMR][1000 genomes]
rs3130450	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3130451	0.89[ASN][1000 genomes]
rs3130452	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3130498	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130499	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3130500	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3130501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3130502	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130503	0.86[AMR][1000 genomes]
rs3130504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130575	0.95[EUR][1000 genomes]
rs3130928	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3130929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3130931	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3130932	0.83[ASN][1000 genomes]
rs3130934	0.82[ASN][1000 genomes]
rs3132523	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132524	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132528	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3132535	0.88[ASN][1000 genomes]
rs9263804	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv1019637	chr6:31104401-31354706	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
13	nsv1029569	chr6:31104401-31412740	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
14	nsv538174	chr6:31104401-31412740	Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
15	nsv1034391	chr6:31131121-31279595	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
16	nsv1025909	chr6:31131121-31354706	Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
17	nsv538175	chr6:31131121-31354706	Active TSS Bivalent Enhancer Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
18	nsv1015890	chr6:31131121-31449207	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
19	nsv538176	chr6:31131121-31449207	Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3132522	HLA-C///LOC732037	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31127200-31140600	Weak transcription	Left Ventricle	heart
2	chr6:31127200-31146800	Weak transcription	Small Intestine	intestine
3	chr6:31127600-31143000	Weak transcription	Right Ventricle	heart
4	chr6:31127600-31147800	Weak transcription	Primary B cells from cord blood	blood
5	chr6:31127600-31148000	Weak transcription	Right Atrium	heart
6	chr6:31127800-31142800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:31127800-31142800	Weak transcription	HSMM	muscle
8	chr6:31127800-31146200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:31127800-31147800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:31127800-31147800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:31127800-31153200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:31128000-31140400	Weak transcription	Brain Germinal Matrix	brain
13	chr6:31128000-31143200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:31128200-31143600	Weak transcription	NHDF-Ad	bronchial
15	chr6:31130200-31146200	Weak transcription	Lung	lung
16	chr6:31130400-31147800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:31130600-31146800	Weak transcription	Colonic Mucosa	Colon
18	chr6:31130800-31141800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:31131000-31141000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:31131000-31143200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:31131000-31143400	Weak transcription	Esophagus	oesophagus
22	chr6:31131000-31147800	Weak transcription	Adipose Nuclei	Adipose
23	chr6:31131000-31148000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:31131000-31148000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:31131200-31143600	Weak transcription	Osteobl	bone
26	chr6:31131400-31142800	Weak transcription	HepG2	liver
27	chr6:31131600-31143400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:31131600-31143400	Weak transcription	Fetal Lung	lung
29	chr6:31131600-31143600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:31131800-31138200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:31131800-31141200	Weak transcription	A549	lung
32	chr6:31132000-31137800	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:31132000-31140200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:31132000-31148000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:31133000-31143800	Weak transcription	Dnd41	blood
36	chr6:31133000-31148000	Weak transcription	Thymus	Thymus
37	chr6:31133000-31148200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:31133600-31143000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:31133600-31143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:31134200-31140200	Weak transcription	Pancreas	Pancrea
41	chr6:31134200-31145800	Weak transcription	GM12878-XiMat	blood
42	chr6:31135000-31138600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr6:31135000-31143400	Weak transcription	Fetal Thymus	thymus
44	chr6:31135400-31138600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr6:31135800-31138600	Active TSS	H1 Cell Line	embryonic stem cell
46	chr6:31135800-31139000	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr6:31136000-31137800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:31136200-31137800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:31136200-31138400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:31136200-31138600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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