Variant report

Variant	rs17131292
Chromosome Location	chr1:70876959-70876960
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:406)
CpG islands
(count:122)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:406 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

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	RAD21	chr1:70876800-70877082	SK-N-SH_RA	brain:	n/a	n/a
5	NFYA	chr1:70876358-70877085	K562	blood:	n/a	chr1:70876831-70876841 chr1:70876829-70876843 chr1:70876829-70876847 chr1:70876829-70876844 chr1:70876829-70876844
6	ZNF384	chr1:70876878-70877088	GM12878	blood:	n/a	n/a
7	SIN3A	chr1:70876090-70878048	H1-hESC	embryonic stem cell:	n/a	n/a
8	MAFK	chr1:70876280-70877955	Hela-S3	cervix:	n/a	n/a
9	TAF7	chr1:70875981-70877337	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAFK	chr1:70876265-70877307	IMR90	lung:	n/a	n/a
11	POLR2A	chr1:70876246-70877189	HepG2	liver:	n/a	n/a
12	PAX5	chr1:70876273-70877091	GM12878	blood:	n/a	n/a
13	TAF1	chr1:70876349-70877087	HepG2	liver:	n/a	n/a
14	NR2F2	chr1:70876121-70877231	K562	blood:	n/a	n/a
15	MAX	chr1:70876264-70877419	K562	blood:	n/a	n/a
16	HDAC2	chr1:70876470-70877229	H1-hESC	embryonic stem cell:	n/a	n/a
17	ARID3A	chr1:70876387-70877951	HepG2	liver:	n/a	n/a
18	POLR2A	chr1:70876202-70877340	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr1:70876186-70877322	GM12878	blood:	n/a	n/a
20	REST	chr1:70876881-70877360	K562	blood:	n/a	n/a
21	MAZ	chr1:70876259-70877494	K562	blood:	n/a	n/a
22	REST	chr1:70876419-70877232	H1-neurons	neurons:	n/a	chr1:70876782-70876795
23	POLR2A	chr1:70876214-70877385	HL-60	blood:	n/a	n/a
24	BRCA1	chr1:70876020-70878123	Hela-S3	cervix:	n/a	n/a
25	NFYA	chr1:70876425-70877213	Hela-S3	cervix:	n/a	chr1:70876831-70876841 chr1:70876829-70876843 chr1:70876829-70876847 chr1:70876829-70876844 chr1:70876829-70876844
26	POLR2A	chr1:70876320-70877212	PANC-1	pancreas:	n/a	n/a
27	GTF2F1	chr1:70876554-70877163	K562	blood:	n/a	n/a
28	TAF1	chr1:70876368-70877398	ECC-1	luminal epithelium:	n/a	n/a
29	SIN3AK20	chr1:70876569-70877319	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:70876212-70877149	HepG2	liver:	n/a	n/a
31	RCOR1	chr1:70876136-70877245	GM12878	blood:	n/a	n/a
32	TAF1	chr1:70876204-70877341	H1-hESC	embryonic stem cell:	n/a	n/a
33	MXI1	chr1:70876311-70877311	GM12878	blood:	n/a	n/a
34	MXI1	chr1:70876224-70878144	Hela-S3	cervix:	n/a	n/a
35	ATF2	chr1:70876164-70877171	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr1:70875929-70877354	K562	blood:	n/a	n/a
37	MAX	chr1:70876298-70877389	MCF-7	breast:	n/a	n/a
38	POLR2A	chr1:70876245-70877205	GM19099	blood:	n/a	n/a
39	POLR2A	chr1:70876327-70877195	K562	blood:	n/a	n/a
40	CEBPB	chr1:70875817-70878169	Hela-S3	cervix:	n/a	chr1:70877957-70877968
41	MXI1	chr1:70876344-70877193	K562	blood:	n/a	n/a
42	HEY1	chr1:70876290-70877165	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:70876074-70877327	Raji	blood:	n/a	n/a
44	POLR2A	chr1:70876083-70878032	Hela-S3	cervix:	n/a	n/a
45	TBL1XR1	chr1:70876312-70877461	K562	blood:	n/a	n/a
46	POLR2A	chr1:70876277-70877316	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:70876474-70877141	A549	lung:	n/a	n/a
48	MAX	chr1:70876224-70877412	H1-hESC	embryonic stem cell:	n/a	n/a
49	TBP	chr1:70876275-70877170	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:70876238-70877283	GM19193	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:70876918-70876968	NB4	blood:	n/a
2	chr1:70876953-70877003	T-47D	breast:	n/a
3	chr1:70876918-70876968	AG10803	skin:	n/a
4	chr1:70876953-70877003	HCF	heart:	n/a
5	chr1:70876953-70877003	HNPCEpiC	eye:	n/a
6	chr1:70876953-70877003	ovcar-3	ovarian:	n/a
7	chr1:70876953-70877003	AG04450	lung:	fetal
8	chr1:70876918-70876968	HEK293	kidney:	embryo
9	chr1:70876953-70877003	ProgFib	skin:	n/a
10	chr1:70876918-70876968	ProgFib	skin:	n/a
11	chr1:70876953-70877003	CMK	blood:	n/a
12	chr1:70876953-70877003	SK-N-SH	brain:	n/a
13	chr1:70876918-70876968	NHBE	bronchial:	n/a
14	chr1:70876953-70877003	ECC-1	luminal epithelium:	n/a
15	chr1:70876918-70876968	AG09319	gingival:	n/a
16	chr1:70876953-70877003	NB4	blood:	n/a
17	chr1:70876918-70876968	NH-A	brain:	n/a
18	chr1:70876953-70877003	SK-N-MC	brain:	n/a
19	chr1:70876918-70876968	GM12892	blood:	n/a
20	chr1:70876953-70877003	PANC-1	pancreas:	n/a
21	chr1:70876953-70877003	IMR90	lung:	fetal
22	chr1:70876918-70876968	GM06990	blood:	n/a
23	chr1:70876953-70877003	NHDF-neo	bronchial:	n/a
24	chr1:70876953-70877003	SK-N-SH_RA	brain:	n/a
25	chr1:70876953-70877003	MCF-7	breast:	n/a
26	chr1:70876918-70876968	AG04449	skin:	fetal
27	chr1:70876918-70876968	RPTEC	kidney:	n/a
28	chr1:70876953-70877003	HEEpiC	esophagus:	n/a
29	chr1:70876953-70877003	GM12891	blood:	n/a
30	chr1:70876918-70876968	GM12891	blood:	n/a
31	chr1:70876918-70876968	BJ	skin:	n/a
32	chr1:70876953-70877003	K562	blood:	n/a
33	chr1:70876953-70877003	HEK293	kidney:	embryo
34	chr1:70876953-70877003	PrEC	prostate:	n/a
35	chr1:70876953-70877003	AG09319	gingival:	n/a
36	chr1:70876918-70876968	NT2-D1	testis:	n/a
37	chr1:70876953-70877003	HUVEC	blood vessel:	n/a
38	chr1:70876918-70876968	HCM	heart:	n/a
39	chr1:70876918-70876968	HAEpiC	amniotic membrane:	n/a
40	chr1:70876918-70876968	PANC-1	pancreas:	n/a
41	chr1:70876953-70877003	MCF10A-Er-Src	breast:	n/a
42	chr1:70876953-70877003	NT2-D1	testis:	n/a
43	chr1:70876918-70876968	K562	blood:	n/a
44	chr1:70876918-70876968	ECC-1	luminal epithelium:	n/a
45	chr1:70876953-70877003	SAEC	small airway:	n/a
46	chr1:70876918-70876968	HCT-116	colon:	n/a
47	chr1:70876918-70876968	AG04450	lung:	fetal
48	chr1:70876953-70877003	HCM	heart:	n/a
49	chr1:70876953-70877003	GM19239	blood:	n/a
50	chr1:70876953-70877003	RPTEC	kidney:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70876680..70877237-chrX:47076703..47077310,2	Hela-S3	cervix:
2	chr1:70876951..70877911-chr1:155196685..155197597,2	Hela-S3	cervix:
3	chr1:70876550..70877428-chr9:127420306..127420837,2	NB4	blood:
4	chr1:70876465..70877378-chr22:43010860..43011843,2	Hela-S3	cervix:
5	chr1:70876503..70877021-chr1:144533689..144534211,2	Hela-S3	cervix:
6	chr1:70876526..70879847-chr1:71510519..71513789,3	K562	blood:
7	chr1:70876562..70877348-chr2:44223071..44223588,2	Hela-S3	cervix:
8	chr1:70876874..70877654-chr11:62608483..62609471,3	Hela-S3	cervix:
9	chr1:70876737..70877459-chr17:39844968..39845649,2	Hela-S3	cervix:
10	chr1:70876855..70877420-chr11:65728563..65729238,2	Hela-S3	cervix:
11	chr1:70876314..70877183-chr7:30065902..30066426,2	Hela-S3	cervix:
12	chr1:70876707..70877432-chr16:20817683..20818263,2	Hela-S3	cervix:
13	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
14	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:
15	chr1:70779446..70781152-chr1:70876074..70878497,2	MCF-7	breast:
16	chr1:70876400..70877374-chr15:85259317..85260196,2	Hela-S3	cervix:
17	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:

No data

Variant related genes	Relation type
CTH	TF binding region
CTH	CpG island
ENSG00000118454	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000175467	Chromatin interaction
ENSG00000140612	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000050628	Chromatin interaction
ENSG00000173812	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000224020	Chromatin interaction
ENSG00000201699	Chromatin interaction
ENSG00000196678	Chromatin interaction
ENSG00000005189	Chromatin interaction
ENSG00000160766	Chromatin interaction
ENSG00000138095	Chromatin interaction
ENSG00000102225	Chromatin interaction
ENSG00000106080	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11803222	1.00[EUR][1000 genomes]
rs17131260	1.00[EUR][1000 genomes]
rs17131261	0.89[YRI][hapmap]
rs17131275	0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17131277	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17131278	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17131280	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131282	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131286	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131287	0.90[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131288	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17131289	0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57217591	1.00[AMR][1000 genomes]
rs58518248	1.00[AMR][1000 genomes]
rs59320305	1.00[AMR][1000 genomes]
rs59856193	1.00[EUR][1000 genomes]
rs6413468	0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72914697	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72914698	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72916616	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72916621	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72929301	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931203	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72931208	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7549628	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
rs17131292	HHLA3	cis	multi-tissue	Pritchard

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	chr1:70875800-70877600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:70875800-70877800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:70875800-70878800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:70875800-70878800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:70875800-70879000	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:70875800-70879000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:70875800-70879000	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr1:70875800-70879800	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:70875800-70880000	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:70876000-70877200	Active TSS	Fetal Muscle Trunk	muscle
12	chr1:70876000-70877200	Active TSS	Thymus	Thymus
13	chr1:70876000-70877400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:70876000-70877400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:70876000-70877400	Active TSS	Brain Cingulate Gyrus	brain
16	chr1:70876000-70877400	Active TSS	Colon Smooth Muscle	Colon
17	chr1:70876000-70877400	Active TSS	Duodenum Mucosa	Duodenum
18	chr1:70876000-70877600	Active TSS	Brain Germinal Matrix	brain
19	chr1:70876000-70877600	Active TSS	Fetal Kidney	kidney
20	chr1:70876000-70877600	Active TSS	Fetal Stomach	stomach
21	chr1:70876000-70877600	Active TSS	Left Ventricle	heart
22	chr1:70876000-70877800	Active TSS	Fetal Brain Male	brain
23	chr1:70876000-70877800	Active TSS	Stomach Mucosa	stomach
24	chr1:70876000-70878000	Bivalent/Poised TSS	HepG2	liver
25	chr1:70876000-70878200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:70876000-70878200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:70876000-70878200	Active TSS	Aorta	Aorta
29	chr1:70876000-70878200	Active TSS	Colonic Mucosa	Colon
30	chr1:70876000-70878200	Active TSS	Psoas Muscle	Psoas
31	chr1:70876000-70878200	Active TSS	GM12878-XiMat	blood
32	chr1:70876000-70878400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:70876000-70878400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:70876000-70878400	Active TSS	Duodenum Smooth Muscle	Duodenum
35	chr1:70876000-70878400	Active TSS	Fetal Intestine Large	intestine
36	chr1:70876000-70878600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:70876000-70878600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:70876000-70878600	Active TSS	Ovary	ovary
39	chr1:70876000-70878600	Active TSS	Right Atrium	heart
40	chr1:70876000-70878600	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr1:70876000-70878800	Active TSS	H9 Cell Line	embryonic stem cell
42	chr1:70876000-70878800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:70876000-70878800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:70876000-70878800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr1:70876000-70878800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:70876000-70878800	Active TSS	Brain Substantia Nigra	brain
47	chr1:70876000-70878800	Active TSS	Right Ventricle	heart
48	chr1:70876000-70879000	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:70876000-70879000	Active TSS	K562	blood
50	chr1:70876200-70877000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood

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