Variant report

Variant	rs17131261
Chromosome Location	chr1:70820802-70820803
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:352)
CpG islands
(count:61)
Chromatin interactive
region (count:21)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:352 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr1:70820240-70820819	GM12878	blood:	n/a	n/a
2	TAF1	chr1:70819662-70820901	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr1:70820085-70821098	K562	blood:	n/a	n/a
4	MAX	chr1:70820057-70820852	K562	blood:	n/a	chr1:70820464-70820474
5	ATF2	chr1:70820141-70820996	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr1:70820015-70820836	MCF-7	breast:	n/a	n/a
7	SIN3A	chr1:70819043-70820956	H1-hESC	embryonic stem cell:	n/a	chr1:70820145-70820154
8	EP300	chr1:70820237-70821093	K562	blood:	n/a	n/a
9	GABPA	chr1:70820080-70821044	HL-60	blood:	n/a	n/a
10	ELF1	chr1:70819973-70820891	GM12878	blood:	n/a	chr1:70820092-70820101 chr1:70820392-70820403
11	RELA	chr1:70820046-70821128	GM10847	blood:	n/a	n/a
12	YY1	chr1:70819991-70820841	A549	lung:	n/a	chr1:70820092-70820101 chr1:70820382-70820402 chr1:70820386-70820394
13	GATA3	chr1:70820003-70820941	SK-N-SH	brain:	n/a	n/a
14	MXI1	chr1:70820203-70820824	K562	blood:	n/a	n/a
15	TBP	chr1:70819690-70821073	K562	blood:	n/a	n/a
16	GTF2F1	chr1:70820200-70820827	K562	blood:	n/a	n/a
17	MAFK	chr1:70820154-70821052	HepG2	liver:	n/a	n/a
18	MAX	chr1:70819593-70820980	SK-N-SH	brain:	n/a	chr1:70820464-70820474
19	BRCA1	chr1:70820007-70820985	H1-hESC	embryonic stem cell:	n/a	chr1:70820407-70820416
20	BCLAF1	chr1:70820266-70820936	K562	blood:	n/a	n/a
21	RCOR1	chr1:70819921-70821135	K562	blood:	n/a	n/a
22	POLR2A	chr1:70819335-70821040	Hela-S3	cervix:	n/a	n/a
23	USF2	chr1:70820351-70821124	Hela-S3	cervix:	n/a	n/a
24	MTA3	chr1:70819448-70821088	GM12878	blood:	n/a	n/a
25	ELF1	chr1:70819424-70820829	GM12878	blood:	n/a	chr1:70820092-70820101 chr1:70820392-70820403
26	JUND	chr1:70819849-70821087	K562	blood:	n/a	n/a
27	GABPA	chr1:70820196-70821066	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr1:70819409-70820958	GM19193	blood:	n/a	n/a
29	POLR2A	chr1:70819817-70821101	HepG2	liver:	n/a	n/a
30	UBTF	chr1:70819538-70820874	K562	blood:	n/a	n/a
31	STAT1	chr1:70820210-70820828	GM12878	blood:	n/a	chr1:70820489-70820497
32	POLR2A	chr1:70819921-70820863	HL-60	blood:	n/a	n/a
33	TEAD4	chr1:70820081-70821012	K562	blood:	n/a	n/a
34	EP300	chr1:70819912-70820968	ECC-1	luminal epithelium:	n/a	n/a
35	MYC	chr1:70820314-70820839	HUVEC	blood vessel:	n/a	chr1:70820464-70820474
36	NFATC1	chr1:70820181-70820884	GM12878	blood:	n/a	n/a
37	HCFC1	chr1:70819192-70820893	K562	blood:	n/a	n/a
38	ZKSCAN1	chr1:70820047-70820954	Hela-S3	cervix:	n/a	n/a
39	ATF2	chr1:70820147-70821014	GM12878	blood:	n/a	n/a
40	TBL1XR1	chr1:70820308-70821002	K562	blood:	n/a	n/a
41	ZBTB33	chr1:70819913-70820913	A549	lung:	n/a	chr1:70820440-70820455 chr1:70820405-70820420 chr1:70820407-70820416 chr1:70820408-70820418
42	CHD2	chr1:70819276-70821003	K562	blood:	n/a	chr1:70820407-70820416
43	HA-E2F1	chr1:70819906-70820816	Hela-S3	cervix:	n/a	n/a
44	STAT1	chr1:70819593-70820997	Hela-S3	cervix:	n/a	chr1:70820489-70820497 chr1:70819624-70819636 chr1:70820104-70820116
45	POLR2A	chr1:70819400-70820899	GM15510	blood:	n/a	n/a
46	REST	chr1:70820119-70820965	PFSK-1	brain:	n/a	chr1:70820131-70820149
47	POLR2A	chr1:70818813-70821108	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr1:70819206-70821087	GM12892	blood:	n/a	n/a
49	CREB1	chr1:70820460-70820939	A549	lung:	n/a	n/a
50	USF2	chr1:70820257-70820830	GM12878	blood:	n/a	chr1:70820349-70820365

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:70820790-70820840	IMR90	lung:	fetal
2	chr1:70820790-70820840	RPTEC	kidney:	n/a
3	chr1:70820790-70820840	AG10803	skin:	n/a
4	chr1:70820790-70820840	MCF10A-Er-Src	breast:	n/a
5	chr1:70820790-70820840	HIPEpiC	eye:	n/a
6	chr1:70820790-70820840	HMEC	breast:	n/a
7	chr1:70820790-70820840	ProgFib	skin:	n/a
8	chr1:70820790-70820840	HCT-116	colon:	n/a
9	chr1:70820790-70820840	HRPEpiC	eye:	n/a
10	chr1:70820790-70820840	SAEC	small airway:	n/a
11	chr1:70820790-70820840	NHBE	bronchial:	n/a
12	chr1:70820790-70820840	ovcar-3	ovarian:	n/a
13	chr1:70820790-70820840	Caco-2	colon:	n/a
14	chr1:70820790-70820840	AG04450	lung:	fetal
15	chr1:70820790-70820840	PFSK-1	brain:	n/a
16	chr1:70820790-70820840	GM12892	blood:	n/a
17	chr1:70820790-70820840	NHDF-neo	bronchial:	n/a
18	chr1:70820790-70820840	GM06990	blood:	n/a
19	chr1:70820790-70820840	HUVEC	blood vessel:	n/a
20	chr1:70820790-70820840	HPAEpiC	pulmonary alveolar:	n/a
21	chr1:70820790-70820840	A549	lung:	n/a
22	chr1:70820790-70820840	HNPCEpiC	eye:	n/a
23	chr1:70820790-70820840	MCF-7	breast:	n/a
24	chr1:70820790-70820840	K562	blood:	n/a
25	chr1:70820790-70820840	PrEC	prostate:	n/a
26	chr1:70820790-70820840	HCPEpiC	choroid plexus:	n/a
27	chr1:70820790-70820840	HepG2	liver:	n/a
28	chr1:70820790-70820840	Hepatocyte	liver:	n/a
29	chr1:70820790-70820840	HCF	heart:	n/a
30	chr1:70820790-70820840	SKMC	muscle:	n/a
31	chr1:70820790-70820840	GM19239	blood:	n/a
32	chr1:70820790-70820840	HRE	kidney:	n/a
33	chr1:70820790-70820840	AG09309	skin:	n/a
34	chr1:70820790-70820840	HL-60	blood:	n/a
35	chr1:70820790-70820840	AoSMC	blood vessel:	n/a
36	chr1:70820790-70820840	U87	brain:	n/a
37	chr1:70820790-70820840	AG04449	skin:	fetal
38	chr1:70820790-70820840	HAEpiC	amniotic membrane:	n/a
39	chr1:70820790-70820840	HRCEpiC	kidney:	n/a
40	chr1:70820790-70820840	ECC-1	luminal epithelium:	n/a
41	chr1:70820790-70820840	Hela-S3	cervix:	n/a
42	chr1:70820790-70820840	AG09319	gingival:	n/a
43	chr1:70820790-70820840	BE2_C	brain:	n/a
44	chr1:70820790-70820840	HCM	heart:	n/a
45	chr1:70820790-70820840	SK-N-SH	brain:	n/a
46	chr1:70820790-70820840	NT2-D1	testis:	n/a
47	chr1:70820790-70820840	SK-N-MC	brain:	n/a
48	chr1:70820790-70820840	BJ	skin:	n/a
49	chr1:70820790-70820840	NH-A	brain:	n/a
50	chr1:70820790-70820840	SK-N-SH_RA	brain:	n/a

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:70820291..70820901-chr2:219433432..219434034,2	Hela-S3	cervix:
2	chr1:70820369..70820909-chr16:4103767..4104269,2	Hela-S3	cervix:
3	chr1:70686799..70688622-chr1:70819236..70822047,3	K562	blood:
4	chr1:70670191..70673421-chr1:70819814..70822311,3	K562	blood:
5	chr1:70820317..70820900-chr2:204103295..204104099,2	Hela-S3	cervix:
6	chr1:70819015..70821620-chr1:70875663..70878848,3	MCF-7	breast:
7	chr1:70820223..70820900-chr8:22925930..22926635,2	Hela-S3	cervix:
8	chr1:70820287..70820857-chr20:33543072..33543925,2	Hela-S3	cervix:
9	chr1:70820288..70821043-chr14:55878152..55878652,2	Hela-S3	cervix:
10	chr1:70819013..70822302-chr1:70824014..70829303,9	MCF-7	breast:
11	chr1:70820419..70821379-chr6:31794911..31795554,2	Hela-S3	cervix:
12	chr1:70820288..70821087-chr12:13044176..13045013,2	Hela-S3	cervix:
13	chr1:70686799..70689606-chr1:70818481..70820974,3	K562	blood:
14	chr1:70685799..70687948-chr1:70819964..70821804,2	MCF-7	breast:
15	chr1:70820321..70821295-chr16:67693740..67694256,2	Hela-S3	cervix:
16	chr1:70820399..70820978-chr19:1039823..1040333,2	Hela-S3	cervix:
17	chr1:70686924..70688596-chr1:70820161..70821739,2	MCF-7	breast:
18	chr1:70814842..70821925-chr1:70874223..70879265,8	K562	blood:
19	chr1:40506025..40506869-chr1:70820330..70820998,2	Hela-S3	cervix:
20	chr1:70820369..70820950-chr20:18487901..18488870,2	Hela-S3	cervix:
21	chr1:70818087..70822177-chr1:70874224..70879265,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTH-9	chr1:70820511-70820891	NONHSAT003856

No data

Variant related genes	Relation type
ANKRD13C	TF binding region
ANKRD13C	CpG island
ENSG00000120889	Chromatin interaction
ENSG00000064687	Chromatin interaction
ENSG00000131236	Chromatin interaction
ENSG00000228988	Chromatin interaction
ENSG00000162104	Chromatin interaction
ENSG00000126775	Chromatin interaction
ENSG00000144580	Chromatin interaction
ENSG00000204388	Chromatin interaction
ENSG00000100983	Chromatin interaction
ENSG00000102977	Chromatin interaction
ENSG00000116754	Chromatin interaction
ENSG00000226088	Chromatin interaction
ENSG00000013588	Chromatin interaction
ENSG00000116761	Chromatin interaction
ENSG00000119004	Chromatin interaction
ENSG00000101310	Chromatin interaction
ENSG00000066557	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17131275	1.00[YRI][hapmap]
rs17131277	1.00[YRI][hapmap]
rs17131278	1.00[YRI][hapmap]
rs17131280	1.00[YRI][hapmap]
rs17131282	1.00[YRI][hapmap]
rs17131286	1.00[YRI][hapmap]
rs17131287	0.90[YRI][hapmap]
rs17131288	1.00[YRI][hapmap]
rs17131289	1.00[YRI][hapmap]
rs17131292	0.89[YRI][hapmap]
rs6413468	1.00[YRI][hapmap]
rs72929301	0.87[AFR][1000 genomes]
rs72931203	0.87[AFR][1000 genomes]
rs72931208	0.87[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1012563	chr1:70753332-70832118	Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv1801665	chr1:70755511-70832053	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	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
5	esv11736	chr1:70820591-70825114	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17131261	ENSG00000197568	cis	multi-tissue	Pritchard
rs17131261	HHLA3	cis	multi-tissue	Pritchard
rs17131261	HHLA3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70817000-70821000	Active TSS	Fetal Brain Female	brain
2	chr1:70817600-70821200	Active TSS	NHLF	lung
3	chr1:70817600-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:70817600-70821600	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:70817600-70822000	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:70817800-70821400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:70818000-70821200	Active TSS	Brain Hippocampus Middle	brain
8	chr1:70818000-70821400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:70818000-70821400	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:70818000-70821400	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:70818000-70821800	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr1:70818200-70821000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:70818200-70821000	Active TSS	Ovary	ovary
14	chr1:70818200-70821000	Active TSS	HSMM	muscle
15	chr1:70818200-70821200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:70818200-70821200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:70818200-70821200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr1:70818200-70821200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:70818200-70821200	Active TSS	Aorta	Aorta
20	chr1:70818200-70821200	Active TSS	Psoas Muscle	Psoas
21	chr1:70818200-70821200	Active TSS	Right Atrium	heart
22	chr1:70818200-70821200	Active TSS	Stomach Smooth Muscle	stomach
23	chr1:70818200-70821400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:70818200-70821400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:70818200-70821400	Active TSS	A549	lung
26	chr1:70818400-70821000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:70818400-70821000	Active TSS	Fetal Intestine Large	intestine
28	chr1:70818400-70821200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr1:70818400-70821200	Active TSS	H1 Cell Line	embryonic stem cell
30	chr1:70818400-70821400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:70818600-70821000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:70818600-70821200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:70818600-70821200	Active TSS	Fetal Stomach	stomach
34	chr1:70818800-70821200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:70818800-70821200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr1:70818800-70821400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:70819000-70821000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr1:70819000-70821000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:70819000-70821000	Active TSS	Colonic Mucosa	Colon
40	chr1:70819000-70821000	Active TSS	Left Ventricle	heart
41	chr1:70819000-70821200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:70819000-70821200	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:70819000-70821200	Active TSS	Right Ventricle	heart
44	chr1:70819000-70821400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:70819200-70821000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:70819200-70821000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:70819200-70821000	Active TSS	Gastric	stomach
48	chr1:70819200-70821000	Active TSS	Lung	lung
49	chr1:70819200-70821200	Active TSS	Esophagus	oesophagus
50	chr1:70819200-70821200	Active TSS	HUVEC	blood vessel

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