Variant report

Variant	rs17131290
Chromosome Location	chr1:70876569-70876570
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	JUND	chr1:70876178-70878164	K562	blood:	n/a	chr1:70877602-70877612 chr1:70877602-70877612 chr1:70876424-70876435
2	RELA	chr1:70876315-70877354	GM15510	blood:	n/a	n/a
3	BHLHE40	chr1:70876322-70877320	K562	blood:	n/a	n/a
4	NFYA	chr1:70876358-70877085	K562	blood:	n/a	chr1:70876831-70876841 chr1:70876829-70876843 chr1:70876829-70876847 chr1:70876829-70876844 chr1:70876829-70876844
5	SIN3A	chr1:70876090-70878048	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAFK	chr1:70876280-70877955	Hela-S3	cervix:	n/a	n/a
7	TAF7	chr1:70875981-70877337	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr1:70876265-70877307	IMR90	lung:	n/a	n/a
9	POLR2A	chr1:70876246-70877189	HepG2	liver:	n/a	n/a
10	PAX5	chr1:70876273-70877091	GM12878	blood:	n/a	n/a
11	TAF1	chr1:70876349-70877087	HepG2	liver:	n/a	n/a
12	NR2F2	chr1:70876121-70877231	K562	blood:	n/a	n/a
13	MAX	chr1:70876264-70877419	K562	blood:	n/a	n/a
14	HDAC2	chr1:70876470-70877229	H1-hESC	embryonic stem cell:	n/a	n/a
15	CUX1	chr1:70876060-70876733	GM12878	blood:	n/a	n/a
16	ARID3A	chr1:70876387-70877951	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:70876202-70877340	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:70876186-70877322	GM12878	blood:	n/a	n/a
19	MAZ	chr1:70876259-70877494	K562	blood:	n/a	n/a
20	REST	chr1:70876419-70877232	H1-neurons	neurons:	n/a	chr1:70876782-70876795
21	POLR2A	chr1:70876214-70877385	HL-60	blood:	n/a	n/a
22	BRCA1	chr1:70876020-70878123	Hela-S3	cervix:	n/a	n/a
23	NFYA	chr1:70876425-70877213	Hela-S3	cervix:	n/a	chr1:70876831-70876841 chr1:70876829-70876843 chr1:70876829-70876847 chr1:70876829-70876844 chr1:70876829-70876844
24	POLR2A	chr1:70876320-70877212	PANC-1	pancreas:	n/a	n/a
25	GTF2F1	chr1:70876554-70877163	K562	blood:	n/a	n/a
26	TAF1	chr1:70876368-70877398	ECC-1	luminal epithelium:	n/a	n/a
27	SIN3AK20	chr1:70876569-70877319	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:70876212-70877149	HepG2	liver:	n/a	n/a
29	RCOR1	chr1:70876136-70877245	GM12878	blood:	n/a	n/a
30	TAF1	chr1:70876204-70877341	H1-hESC	embryonic stem cell:	n/a	n/a
31	MXI1	chr1:70876311-70877311	GM12878	blood:	n/a	n/a
32	MXI1	chr1:70876224-70878144	Hela-S3	cervix:	n/a	n/a
33	ATF2	chr1:70876164-70877171	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr1:70875929-70877354	K562	blood:	n/a	n/a
35	MAX	chr1:70876298-70877389	MCF-7	breast:	n/a	n/a
36	POLR2A	chr1:70876245-70877205	GM19099	blood:	n/a	n/a
37	POLR2A	chr1:70876327-70877195	K562	blood:	n/a	n/a
38	CEBPB	chr1:70875817-70878169	Hela-S3	cervix:	n/a	chr1:70877957-70877968
39	MXI1	chr1:70876344-70877193	K562	blood:	n/a	n/a
40	HEY1	chr1:70876290-70877165	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:70876074-70877327	Raji	blood:	n/a	n/a
42	POLR2A	chr1:70876083-70878032	Hela-S3	cervix:	n/a	n/a
43	TBL1XR1	chr1:70876312-70877461	K562	blood:	n/a	n/a
44	POLR2A	chr1:70876277-70877316	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:70876474-70877141	A549	lung:	n/a	n/a
46	MAX	chr1:70876224-70877412	H1-hESC	embryonic stem cell:	n/a	n/a
47	TBP	chr1:70876275-70877170	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:70876238-70877283	GM19193	blood:	n/a	n/a
49	FOXA1	chr1:70876307-70877068	HepG2	liver:	n/a	n/a
50	EP300	chr1:70876242-70877123	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:70876550..70877428-chr9:127420306..127420837,2	NB4	blood:
2	chr1:70876465..70877378-chr22:43010860..43011843,2	Hela-S3	cervix:
3	chr1:70876503..70877021-chr1:144533689..144534211,2	Hela-S3	cervix:
4	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
5	chr1:70876562..70877348-chr2:44223071..44223588,2	Hela-S3	cervix:
6	chr1:70876314..70877183-chr7:30065902..30066426,2	Hela-S3	cervix:
7	chr1:70876042..70876746-chr4:89444423..89445254,2	NB4	blood:
8	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
9	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
10	chr1:70779446..70781152-chr1:70876074..70878497,2	MCF-7	breast:
11	chr1:70876400..70877374-chr15:85259317..85260196,2	Hela-S3	cervix:
12	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

Variant related genes	Relation type
CTH	TF binding region
ENSG00000140612	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000138095	Chromatin interaction
ENSG00000106080	Chromatin interaction
ENSG00000224020	Chromatin interaction
ENSG00000050628	Chromatin interaction
ENSG00000138641	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000145337	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000270022	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs17131302	0.82[YRI][hapmap];1.00[AMR][1000 genomes]

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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	esv1797324	chr1:70858435-70876569	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
4	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17131290	HHLA3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70875600-70878000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:70875800-70876600	Active TSS	Primary T cells fromperipheralblood	blood
3	chr1:70875800-70876600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:70875800-70877600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:70875800-70877800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:70875800-70878800	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr1:70875800-70878800	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
9	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr1:70876000-70876600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:70876000-70876600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr1:70876000-70877200	Active TSS	Fetal Muscle Trunk	muscle
16	chr1:70876000-70877200	Active TSS	Thymus	Thymus
17	chr1:70876000-70877400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:70876000-70877400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:70876000-70877400	Active TSS	Brain Cingulate Gyrus	brain
20	chr1:70876000-70877400	Active TSS	Colon Smooth Muscle	Colon
21	chr1:70876000-70877400	Active TSS	Duodenum Mucosa	Duodenum
22	chr1:70876000-70877600	Active TSS	Brain Germinal Matrix	brain
23	chr1:70876000-70877600	Active TSS	Fetal Kidney	kidney
24	chr1:70876000-70877600	Active TSS	Fetal Stomach	stomach
25	chr1:70876000-70877600	Active TSS	Left Ventricle	heart
26	chr1:70876000-70877800	Active TSS	Fetal Brain Male	brain
27	chr1:70876000-70877800	Active TSS	Stomach Mucosa	stomach
28	chr1:70876000-70878000	Bivalent/Poised TSS	HepG2	liver
29	chr1:70876000-70878200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:70876000-70878200	Active TSS	Aorta	Aorta
33	chr1:70876000-70878200	Active TSS	Colonic Mucosa	Colon
34	chr1:70876000-70878200	Active TSS	Psoas Muscle	Psoas
35	chr1:70876000-70878200	Active TSS	GM12878-XiMat	blood
36	chr1:70876000-70878400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:70876000-70878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr1:70876000-70878400	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:70876000-70878400	Active TSS	Fetal Intestine Large	intestine
40	chr1:70876000-70878600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:70876000-70878600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:70876000-70878600	Active TSS	Ovary	ovary
43	chr1:70876000-70878600	Active TSS	Right Atrium	heart
44	chr1:70876000-70878600	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr1:70876000-70878800	Active TSS	H9 Cell Line	embryonic stem cell
46	chr1:70876000-70878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr1:70876000-70878800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:70876000-70878800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:70876000-70878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:70876000-70878800	Active TSS	Brain Substantia Nigra	brain

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