Variant report

Variant	rs1046439
Chromosome Location	chr1:174969271-174969272
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:428)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:428 , 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	BRCA1	chr1:174968282-174969305	GM12878	blood:	n/a	chr1:174968964-174968973
2	MAX	chr1:174968147-174969358	K562	blood:	n/a	n/a
3	POLR2A	chr1:174967583-174969607	K562	blood:	n/a	n/a
4	POLR2A	chr1:174967945-174969663	A549	lung:	n/a	n/a
5	SETDB1	chr1:174968357-174969755	K562	blood:	n/a	n/a
6	TAF1	chr1:174967999-174969541	Hela-S3	cervix:	n/a	n/a
7	BCLAF1	chr1:174967503-174969524	GM12878	blood:	n/a	chr1:174969375-174969388
8	YY1	chr1:174968258-174969360	NT2-D1	testis:	n/a	chr1:174968730-174968750
9	TBP	chr1:174967622-174969868	K562	blood:	n/a	n/a
10	POLR2A	chr1:174967073-174971246	Hela-S3	cervix:	n/a	n/a
11	NRF1	chr1:174968597-174969275	H1-hESC	embryonic stem cell:	n/a	chr1:174968868-174968882
12	SMC3	chr1:174969111-174969276	GM12878	blood:	n/a	n/a
13	PAX5	chr1:174967694-174969561	GM12878	blood:	n/a	n/a
14	MAX	chr1:174967671-174969956	HepG2	liver:	n/a	n/a
15	CBX3	chr1:174967581-174969945	K562	blood:	n/a	n/a
16	NR2F2	chr1:174967458-174969656	K562	blood:	n/a	n/a
17	TCF3	chr1:174968907-174969535	GM12878	blood:	n/a	n/a
18	MAX	chr1:174968067-174969901	A549	lung:	n/a	n/a
19	POLR2A	chr1:174967406-174970037	SK-N-MC	brain:	n/a	n/a
20	MAX	chr1:174967642-174969957	K562	blood:	n/a	n/a
21	POLR2A	chr1:174967565-174969538	HUVEC	blood vessel:	n/a	n/a
22	ELF1	chr1:174968155-174969742	GM12878	blood:	n/a	n/a
23	E2F6	chr1:174968150-174969899	A549	lung:	n/a	chr1:174968592-174968600 chr1:174968589-174968600 chr1:174968592-174968600 chr1:174968590-174968601 chr1:174968593-174968600 chr1:174968591-174968601
24	POLR2A	chr1:174967696-174969825	PBDE	blood:	n/a	n/a
25	POLR2A	chr1:174967690-174969754	GM18951	blood:	n/a	n/a
26	SIN3AK20	chr1:174968397-174969673	PANC-1	pancreas:	n/a	n/a
27	CTCF	chr1:174969200-174969450	SAEC	small airway:	n/a	n/a
28	POLR2A	chr1:174967621-174969881	Hela-S3	cervix:	n/a	n/a
29	ZMIZ1	chr1:174967695-174970006	K562	blood:	n/a	n/a
30	POLR2A	chr1:174965583-174970714	MCF10A-Er-Src	breast:	n/a	n/a
31	HA-E2F1	chr1:174968408-174969627	Hela-S3	cervix:	n/a	chr1:174968592-174968600 chr1:174968589-174968600 chr1:174968592-174968600 chr1:174968590-174968601 chr1:174968593-174968600 chr1:174968591-174968601
32	GATA2	chr1:174967551-174969834	SH-SY5Y	brain:	n/a	chr1:174967989-174968002
33	POLR2A	chr1:174967624-174969543	U87	brain:	n/a	n/a
34	CTCF	chr1:174969074-174969278	MCF-7	breast:	n/a	n/a
35	FOSL2	chr1:174968256-174969294	HepG2	liver:	n/a	n/a
36	USF1	chr1:174968184-174969369	SK-N-SH	brain:	n/a	n/a
37	EP300	chr1:174967539-174969377	K562	blood:	n/a	chr1:174968292-174968306
38	STAT1	chr1:174967755-174969622	GM12878	blood:	n/a	n/a
39	HDAC2	chr1:174969053-174969723	K562	blood:	n/a	n/a
40	MYC	chr1:174967637-174970175	NB4	blood:	n/a	n/a
41	TAF1	chr1:174967717-174969669	A549	lung:	n/a	n/a
42	POLR2A	chr1:174967581-174969844	GM12891	blood:	n/a	n/a
43	ZBTB33	chr1:174968089-174969421	A549	lung:	n/a	n/a
44	RCOR1	chr1:174968278-174970948	K562	blood:	n/a	n/a
45	GABPA	chr1:174967532-174969410	MCF-7	breast:	n/a	chr1:174968868-174968882
46	ELK1	chr1:174968266-174969738	Hela-S3	cervix:	n/a	n/a
47	ETS1	chr1:174967945-174969621	K562	blood:	n/a	n/a
48	MAZ	chr1:174967629-174970325	K562	blood:	n/a	n/a
49	POLR2A	chr1:174969020-174969602	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr1:174968186-174969456	SK-N-SH	brain:	n/a	n/a

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174188636..174191430-chr1:174968395..174970624,2	K562	blood:
2	chr1:174968752..174972930-chr1:174980465..174984788,7	MCF-7	breast:
3	chr1:173835653..173838766-chr1:174968504..174972418,4	K562	blood:
4	chr1:174967181..174971270-chr1:174989768..174994107,8	MCF-7	breast:
5	chr1:174922181..174924698-chr1:174966768..174969386,2	K562	blood:
6	chr1:174944704..174946274-chr1:174968716..174970697,2	MCF-7	breast:
7	chr1:174932418..174935374-chr1:174964535..174970014,5	K562	blood:
8	chr1:174966903..174971287-chr1:174971534..174977740,10	MCF-7	breast:
9	chr1:174968651..174969459-chr5:150460230..150461076,2	HCT-116	colon:
10	chr1:174966455..174979047-chr1:174985921..174994239,29	MCF-7	breast:
11	chr1:174968288..174970676-chr11:69455008..69457923,2	MCF-7	breast:
12	chr1:174968009..174969900-chr6:26032089..26033995,2	K562	blood:
13	chr1:173793432..173795581-chr1:174968236..174969749,2	MCF-7	breast:
14	chr1:174968308..174972682-chr1:174973669..174977278,7	MCF-7	breast:
15	chr1:174967096..174970659-chr1:174981028..174985682,6	MCF-7	breast:
16	chr1:174860980..174862757-chr1:174967700..174969508,2	MCF-7	breast:
17	chr1:174128312..174130705-chr1:174967510..174969928,2	K562	blood:
18	chr1:174968082..174970631-chr17:57918562..57920728,2	MCF-7	breast:
19	chr1:174933583..174936463-chr1:174967523..174970706,3	MCF-7	breast:
20	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:
21	chr1:174840446..174846237-chr1:174965266..174970099,5	MCF-7	breast:
22	chr1:173991491..173993335-chr1:174967508..174969953,3	K562	blood:
23	chr1:174968450..174969613-chr17:7387374..7388128,4	Hela-S3	cervix:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MRPS14-1	chr1:174968731-174969328	NONHSAT007744

No data

Variant related genes	Relation type
CACYBP	TF binding region
ENSG00000120333	Chromatin interaction
ENSG00000145901	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000237249	Chromatin interaction
ENSG00000206659	Chromatin interaction
ENSG00000110092	Chromatin interaction
ENSG00000227373	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000116161	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000229531	Chromatin interaction
ENSG00000152061	Chromatin interaction
ENSG00000137259	Chromatin interaction
ENSG00000181222	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11590474	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs1754355	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1801791	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978053	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105949	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187562	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2187939	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285208	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285210	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2301507	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2987869	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs2987874	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs3018410	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.80[MKK][hapmap]
rs3133270	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs3753563	0.91[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.84[AFR][1000 genomes]
rs4233195	0.91[CHB][hapmap];0.90[CHD][hapmap];0.91[JPT][hapmap]
rs4651238	0.91[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.82[ASN][1000 genomes]
rs6425305	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs6425309	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425310	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665216	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap]
rs6669560	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66700013	0.82[ASN][1000 genomes]
rs7514888	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7538588	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs9804056	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs989423	0.91[CHB][hapmap];0.88[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1001000	chr1:174944208-174978853	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1046439	SLC9A11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174967200-174970000	Active TSS	Left Ventricle	heart
2	chr1:174967400-174970600	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr1:174967400-174971400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:174967400-174971400	Active TSS	GM12878-XiMat	blood
5	chr1:174967600-174970000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:174967600-174970000	Active TSS	Brain Cingulate Gyrus	brain
7	chr1:174967600-174970000	Active TSS	Brain Substantia Nigra	brain
8	chr1:174967600-174970400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:174967600-174970400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:174967600-174970400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:174967600-174970400	Active TSS	Psoas Muscle	Psoas
12	chr1:174967600-174970400	Active TSS	Thymus	Thymus
13	chr1:174967600-174970600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:174967600-174970600	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:174967600-174970600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:174967600-174970600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr1:174967600-174970600	Active TSS	Fetal Brain Female	brain
18	chr1:174967600-174970800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:174967600-174971200	Active TSS	A549	lung
20	chr1:174967600-174971600	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr1:174967600-174971600	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr1:174967800-174969800	Active TSS	Liver	Liver
23	chr1:174967800-174969800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:174967800-174969800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:174967800-174969800	Active TSS	Fetal Kidney	kidney
26	chr1:174967800-174970000	Active TSS	Brain Hippocampus Middle	brain
27	chr1:174967800-174970000	Bivalent/Poised TSS	HepG2	liver
28	chr1:174967800-174970200	Active TSS	Brain Angular Gyrus	brain
29	chr1:174967800-174970200	Active TSS	Colonic Mucosa	Colon
30	chr1:174967800-174970200	Active TSS	Fetal Muscle Trunk	muscle
31	chr1:174967800-174970200	Active TSS	Right Ventricle	heart
32	chr1:174967800-174970400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:174967800-174970400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:174967800-174970400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:174967800-174970400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:174967800-174970400	Active TSS	Aorta	Aorta
37	chr1:174967800-174970400	Active TSS	Fetal Intestine Large	intestine
38	chr1:174967800-174970600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr1:174967800-174970600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:174967800-174970600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:174967800-174970800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:174967800-174970800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:174967800-174970800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:174967800-174971000	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:174967800-174971400	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr1:174968000-174969800	Active TSS	Primary T cells from cord blood	blood
47	chr1:174968000-174969800	Active TSS	Gastric	stomach
48	chr1:174968000-174970000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:174968000-174970000	Active TSS	Esophagus	oesophagus
50	chr1:174968000-174970000	Active TSS	Pancreas	Pancrea

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