Variant report

Variant	rs415434
Chromosome Location	chr6:149772645-149772646
allele	C/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	POLR2A	chr6:149772385-149772707	Hela-S3	cervix:	n/a	n/a
2	TFAP2C	chr6:149771572-149773122	Hela-S3	cervix:	n/a	n/a
3	MAZ	chr6:149772414-149772820	Hela-S3	cervix:	n/a	chr6:149772703-149772713
4	SMARCB1	chr6:149771406-149773213	Hela-S3	cervix:	n/a	n/a
5	MAX	chr6:149772401-149772790	Hela-S3	cervix:	n/a	chr6:149772703-149772713
6	POLR2A	chr6:149772582-149772879	Hela-S3	cervix:	n/a	n/a
7	ZKSCAN1	chr6:149772612-149772801	Hela-S3	cervix:	n/a	n/a
8	CHD2	chr6:149772508-149772792	Hela-S3	cervix:	n/a	chr6:149772657-149772667
9	POLR2A	chr6:149772412-149772835	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr6:149771989-149773037	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:149767445..149770252-chr6:149772541..149774258,2	MCF-7	breast:
2	chr6:149769726..149773853-chr6:149775332..149778151,3	K562	blood:
3	chr6:149399709..149402380-chr6:149772394..149774498,2	K562	blood:

Variant related genes	Relation type
ZC3H12D	TF binding region
ENSG00000178199	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11155641	0.80[AFR][1000 genomes]
rs11155644	0.84[AFR][1000 genomes]
rs237003	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs237005	0.86[ASN][1000 genomes]
rs237009	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs237010	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs237012	0.85[EUR][1000 genomes]
rs237016	0.90[EUR][1000 genomes]
rs237018	0.89[EUR][1000 genomes]
rs237019	0.83[EUR][1000 genomes]
rs237024	0.84[AFR][1000 genomes]
rs366905	0.90[EUR][1000 genomes]
rs372238	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs384334	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs394563	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs399673	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs409099	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs409111	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs412894	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs420099	0.86[ASN][1000 genomes]
rs420430	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs421453	0.81[ASN][1000 genomes]
rs438852	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs444784	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs447025	0.85[ASN][1000 genomes]
rs448420	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs448874	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs480870	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548848	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs805026	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv470866	chr6:149744632-149806552	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5533	chr6:149748047-149793072	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv464076	chr6:149755695-149798835	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv604846	chr6:149755695-149798835	ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3355637	chr6:149769659-149774457	Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv3374188	chr6:149770709-149773207	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv3358166	chr6:149771284-149774132	Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149766600-149773000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr6:149767400-149772800	Weak transcription	HepG2	liver
3	chr6:149768400-149779400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:149769600-149782800	Strong transcription	Primary B cells from peripheral blood	blood
5	chr6:149769600-149787200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:149769800-149779800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:149770000-149773000	Weak transcription	Primary B cells from cord blood	blood
8	chr6:149770000-149779600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:149770000-149785200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:149771000-149773400	Enhancers	Fetal Heart	heart
11	chr6:149771400-149773200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr6:149771400-149773200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
13	chr6:149771400-149773400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
14	chr6:149771400-149773400	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:149771600-149772800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:149771600-149772800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:149771600-149772800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:149771600-149772800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
19	chr6:149771600-149772800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:149771600-149772800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr6:149771600-149773000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
22	chr6:149771600-149773000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:149771600-149773000	Bivalent/Poised TSS	Fetal Brain Female	brain
24	chr6:149771600-149773200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:149771600-149773200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:149771600-149773200	Flanking Active TSS	Colonic Mucosa	Colon
27	chr6:149771600-149773200	Bivalent Enhancer	Fetal Brain Male	brain
28	chr6:149771600-149773400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:149771600-149778000	Weak transcription	GM12878-XiMat	blood
30	chr6:149771800-149772800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
31	chr6:149771800-149772800	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:149771800-149772800	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr6:149771800-149772800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
34	chr6:149771800-149772800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:149771800-149772800	Active TSS	Aorta	Aorta
36	chr6:149771800-149772800	Active TSS	Brain Anterior Caudate	brain
37	chr6:149771800-149772800	Active TSS	Colon Smooth Muscle	Colon
38	chr6:149771800-149773000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr6:149771800-149773000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr6:149771800-149773000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:149771800-149773000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr6:149771800-149773000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:149771800-149773000	Active TSS	Brain Substantia Nigra	brain
44	chr6:149771800-149775600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:149771800-149775800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr6:149772000-149772800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr6:149772000-149772800	Active TSS	Duodenum Mucosa	Duodenum
48	chr6:149772000-149772800	Active TSS	Fetal Intestine Large	intestine
49	chr6:149772000-149772800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:149772000-149772800	Active TSS	Right Atrium	heart

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