Variant report

Variant	rs9430648
Chromosome Location	chr1:9749935-9749936
allele	G/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	HMGN3	chr1:9749062-9750237	K562	blood:	n/a	n/a
2	MAX	chr1:9749927-9750337	H1-hESC	embryonic stem cell:	n/a	chr1:9749944-9749954
3	SIN3A	chr1:9748978-9750817	H1-hESC	embryonic stem cell:	n/a	chr1:9750298-9750311 chr1:9750560-9750574
4	MAX	chr1:9749876-9750514	ECC-1	luminal epithelium:	n/a	chr1:9749944-9749954
5	FOXA2	chr1:9749832-9750452	A549	lung:	n/a	n/a
6	ZBTB7A	chr1:9748993-9750468	ECC-1	luminal epithelium:	n/a	chr1:9749244-9749253
7	POLR2A	chr1:9749122-9750384	H1-hESC	embryonic stem cell:	n/a	n/a
8	ZBTB7A	chr1:9749097-9750357	K562	blood:	n/a	chr1:9749244-9749253
9	E2F6	chr1:9749924-9750162	K562	blood:	n/a	n/a
10	MAX	chr1:9749823-9750419	K562	blood:	n/a	chr1:9749944-9749954
11	REST	chr1:9749817-9750595	H1-neurons	neurons:	n/a	chr1:9750561-9750575
12	ZBTB7A	chr1:9749823-9750380	ECC-1	luminal epithelium:	n/a	n/a
13	ZBTB7A	chr1:9749929-9750335	K562	blood:	n/a	n/a
14	MAX	chr1:9749921-9750334	H1-hESC	embryonic stem cell:	n/a	chr1:9749944-9749954
15	E2F6	chr1:9749169-9750301	K562	blood:	n/a	chr1:9749756-9749765
16	MAZ	chr1:9749031-9750486	K562	blood:	n/a	chr1:9749944-9749954
17	MXI1	chr1:9749199-9750294	HepG2	liver:	n/a	chr1:9749721-9749736
18	ELF1	chr1:9749891-9750379	GM12878	blood:	n/a	chr1:9750061-9750070
19	MXI1	chr1:9749554-9750137	H1-hESC	embryonic stem cell:	n/a	chr1:9749721-9749736
20	MAZ	chr1:9746682-9751668	IMR90	lung:	n/a	chr1:9747639-9747648 chr1:9749944-9749954 chr1:9747642-9747652
21	MXI1	chr1:9749567-9750083	K562	blood:	n/a	chr1:9749721-9749736
22	MAX	chr1:9749886-9750413	ECC-1	luminal epithelium:	n/a	chr1:9749944-9749954

No.	Distal block	Cell Line	Cell type
1	chr1:9749593..9751802-chr1:9777886..9780307,2	K562	blood:
2	chr1:9692182..9693930-chr1:9748451..9750202,2	K562	blood:
3	chr1:9746126..9748956-chr1:9749457..9751271,2	MCF-7	breast:
4	chr1:9745914..9747829-chr1:9748443..9751067,2	K562	blood:
5	chr1:9749103..9751299-chr1:9843003..9845112,2	K562	blood:
6	chr1:9712578..9717626-chr1:9745796..9749976,6	K562	blood:
7	chr1:9748418..9751556-chr1:9755069..9757789,4	K562	blood:
8	chr1:9746141..9751802-chr1:9775034..9783332,13	K562	blood:
9	chr1:9686883..9687545-chr1:9749890..9750740,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231789	TF binding region
ENSG00000171608	Chromatin interaction
ENSG00000179840	Chromatin interaction
ENSG00000231789	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4240910	0.95[EUR][1000 genomes]
rs4333853	0.89[EUR][1000 genomes]
rs4420084	0.83[EUR][1000 genomes]
rs4601595	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4846192	0.90[EUR][1000 genomes]
rs4846194	0.90[EUR][1000 genomes]
rs6669509	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9430635	0.89[EUR][1000 genomes]
rs9430636	0.88[EUR][1000 genomes]
rs9430640	0.88[EUR][1000 genomes]
rs9430641	0.89[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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv3408612	chr1:9748390-9751238	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3426414	chr1:9748415-9751113	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	esv3424708	chr1:9748735-9771466	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3338032	chr1:9749165-9750613	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9746800-9750600	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:9747000-9750400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:9747000-9750400	Active TSS	HSMM	muscle
4	chr1:9747000-9751200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr1:9747200-9750400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:9747200-9750400	Active TSS	Aorta	Aorta
7	chr1:9747200-9750600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:9747400-9750200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:9747800-9750400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:9748600-9750000	Bivalent/Poised TSS	Colonic Mucosa	Colon
11	chr1:9748600-9750600	Active TSS	Right Atrium	heart
12	chr1:9748600-9750600	Active TSS	NHLF	lung
13	chr1:9748800-9750000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:9748800-9750400	Active TSS	HSMMtube	muscle
15	chr1:9748800-9750600	Active TSS	Rectal Smooth Muscle	rectum
16	chr1:9749000-9750200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:9749000-9750200	Active TSS	Ovary	ovary
18	chr1:9749000-9750400	Active TSS	Lung	lung
19	chr1:9749000-9750400	Active TSS	A549	lung
20	chr1:9749000-9750800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr1:9749000-9751600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:9749200-9750000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:9749200-9750000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:9749200-9750000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr1:9749200-9750000	Active TSS	Small Intestine	intestine
26	chr1:9749200-9750000	Active TSS	NHDF-Ad	bronchial
27	chr1:9749200-9750200	Active TSS	H1 Cell Line	embryonic stem cell
28	chr1:9749200-9750200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:9749200-9750200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:9749200-9750200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:9749200-9750200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr1:9749200-9750200	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr1:9749200-9750200	Active TSS	Colon Smooth Muscle	Colon
34	chr1:9749200-9750200	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:9749200-9750200	Active TSS	Hela-S3	cervix
36	chr1:9749200-9750200	Active TSS	HepG2	liver
37	chr1:9749200-9750200	Active TSS	K562	blood
38	chr1:9749200-9750200	Active TSS	NHEK	skin
39	chr1:9749200-9750400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:9749200-9750400	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:9749200-9750400	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:9749200-9750400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:9749200-9750400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr1:9749200-9750600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:9749200-9750600	Enhancers	Fetal Heart	heart
46	chr1:9749200-9750800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
47	chr1:9749200-9751000	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr1:9749200-9751000	Active TSS	Fetal Brain Female	brain
49	chr1:9749400-9750000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:9749400-9750000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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