Variant report

Variant	rs10066669
Chromosome Location	chr5:179050918-179050919
allele	C/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	EGR1	chr5:179050693-179051122	K562	blood:	n/a	chr5:179050880-179050889 chr5:179050721-179050730 chr5:179050774-179050783 chr5:179050941-179050950
2	FOXA1	chr5:179050344-179050983	HepG2	liver:	n/a	n/a
3	STAT3	chr5:179050723-179051118	MCF10A-Er-Src	breast:	n/a	n/a
4	TBP	chr5:179050311-179051150	GM12878	blood:	n/a	n/a
5	EGR1	chr5:179050428-179051154	K562	blood:	n/a	chr5:179050880-179050889 chr5:179050721-179050730 chr5:179050774-179050783 chr5:179050941-179050950
6	POLR2A	chr5:179049682-179051896	K562	blood:	n/a	n/a
7	REST	chr5:179050205-179051361	H1-neurons	neurons:	n/a	chr5:179050524-179050537 chr5:179050524-179050544 chr5:179050527-179050540
8	POLR2A	chr5:179049958-179051787	GM12891	blood:	n/a	n/a
9	MAX	chr5:179049581-179052171	K562	blood:	n/a	n/a
10	POLR2A	chr5:179047206-179051952	GM12878	blood:	n/a	n/a
11	TCF12	chr5:179050050-179051441	ECC-1	luminal epithelium:	n/a	chr5:179050732-179050739
12	TCF12	chr5:179049564-179051398	A549	lung:	n/a	chr5:179050732-179050739
13	TBP	chr5:179050438-179051837	Hela-S3	cervix:	n/a	n/a
14	EP300	chr5:179049688-179051279	ECC-1	luminal epithelium:	n/a	chr5:179050405-179050414 chr5:179050982-179050998
15	YY1	chr5:179049647-179051700	GM12892	blood:	n/a	chr5:179051234-179051245 chr5:179050403-179050412 chr5:179050398-179050408 chr5:179050406-179050420 chr5:179051155-179051164
16	CTCF	chr5:179050550-179051092	K562	blood:	n/a	chr5:179050800-179050813 chr5:179050803-179050816
17	CREB1	chr5:179050419-179051015	A549	lung:	n/a	n/a
18	MAX	chr5:179049681-179051857	Hela-S3	cervix:	n/a	n/a
19	CEBPB	chr5:179050426-179051122	MCF-7	breast:	n/a	n/a
20	MAZ	chr5:179049655-179052146	K562	blood:	n/a	n/a
21	POLR2A	chr5:179049656-179052058	K562	blood:	n/a	n/a
22	POLR2A	chr5:179049713-179051451	H1-neurons	neurons:	n/a	n/a
23	CREB1	chr5:179050251-179051285	H1-hESC	embryonic stem cell:	n/a	n/a
24	IRF1	chr5:179050417-179051208	K562	blood:	n/a	chr5:179050740-179050754
25	POLR2A	chr5:179050099-179051751	HepG2	liver:	n/a	n/a
26	TBL1XR1	chr5:179050254-179051271	K562	blood:	n/a	n/a
27	SMC3	chr5:179050321-179051090	Hela-S3	cervix:	n/a	n/a
28	E2F6	chr5:179050534-179051604	H1-hESC	embryonic stem cell:	n/a	chr5:179050941-179050950 chr5:179050880-179050889 chr5:179050774-179050783 chr5:179050891-179050905 chr5:179051155-179051164 chr5:179050721-179050730
29	POLR2A	chr5:179049692-179051794	HUVEC	blood vessel:	n/a	n/a
30	NFYA	chr5:179050627-179051098	Hela-S3	cervix:	n/a	n/a
31	TAF1	chr5:179050389-179051372	Hela-S3	cervix:	n/a	n/a
32	E2F4	chr5:179050377-179051049	GM12878	blood:	n/a	chr5:179050941-179050950 chr5:179050880-179050889 chr5:179050888-179050899 chr5:179050774-179050783 chr5:179050891-179050905 chr5:179050417-179050426 chr5:179050721-179050730 chr5:179050801-179050812
33	FOXP2	chr5:179050482-179051023	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr5:179049295-179051786	MCF10A-Er-Src	breast:	n/a	n/a
35	CREB1	chr5:179049564-179051780	HepG2	liver:	n/a	n/a
36	PML	chr5:179049576-179051610	MCF-7	breast:	n/a	n/a
37	POLR2A	chr5:179049984-179051776	GM12891	blood:	n/a	n/a
38	HCFC1	chr5:179049700-179051326	K562	blood:	n/a	n/a
39	ZNF263	chr5:179050074-179051594	HEK293-T-REx	kidney:	n/a	n/a
40	POLR2A	chr5:179049950-179051791	Hela-S3	cervix:	n/a	n/a
41	MAX	chr5:179050447-179051825	HepG2	liver:	n/a	n/a
42	CEBPB	chr5:179050561-179050975	HepG2	liver:	n/a	n/a
43	STAT1	chr5:179050436-179051225	GM12878	blood:	n/a	n/a
44	REST	chr5:179050450-179050979	K562	blood:	n/a	chr5:179050524-179050537 chr5:179050524-179050544 chr5:179050527-179050540
45	POLR2A	chr5:179050876-179051849	H1-hESC	embryonic stem cell:	n/a	n/a
46	ATF3	chr5:179050328-179050988	A549	lung:	n/a	chr5:179050860-179050868 chr5:179050453-179050462 chr5:179050752-179050763 chr5:179050752-179050763
47	ELF1	chr5:179050238-179051356	GM12878	blood:	n/a	chr5:179051306-179051317
48	NFIC	chr5:179049947-179051552	GM12878	blood:	n/a	n/a
49	WRNIP1	chr5:179050492-179051114	GM12878	blood:	n/a	n/a
50	POLR2A	chr5:179050004-179051380	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179050364..179050918-chrX:23925311..23926248,2	Hela-S3	cervix:
2	chr15:69753495..69755844-chr5:179048677..179051620,2	MCF-7	breast:
3	chr15:101834614..101835570-chr5:179050040..179051063,4	Hela-S3	cervix:
4	chr5:178993088..178996882-chr5:179048174..179052059,4	K562	blood:
5	chr3:135915193..135916031-chr5:179050193..179051036,2	Hela-S3	cervix:
6	chr15:41836411..41836975-chr5:179050328..179051025,2	HCT-116	colon:
7	chr5:179047581..179051358-chr5:179102429..179108878,16	K562	blood:
8	chr5:179050470..179051106-chr9:128469032..128469737,2	HCT-116	colon:
9	chr1:152019751..152020609-chr5:179050208..179051005,2	Hela-S3	cervix:
10	chr11:67777145..67777897-chr5:179050213..179051026,2	Hela-S3	cervix:
11	chr5:179049088..179052063-chr5:179245796..179250145,6	MCF-7	breast:
12	chr5:179003044..179005228-chr5:179048934..179051877,3	K562	blood:
13	chr5:179047278..179052613-chr5:179246048..179251997,13	K562	blood:
14	chr10:75011910..75012711-chr5:179050548..179051140,2	Hela-S3	cervix:
15	chr5:179049356..179051389-chr5:179221894..179224407,2	MCF-7	breast:
16	chr5:178985192..178988541-chr5:179048594..179052191,5	MCF-7	breast:
17	chr1:44411130..44412112-chr5:179050533..179051528,2	Hela-S3	cervix:
18	chr5:179013908..179017053-chr5:179048415..179051520,3	K562	blood:
19	chr5:178882272..178884920-chr5:179049238..179052060,2	K562	blood:
20	chr5:178976591..178978128-chr5:179049452..179051597,2	MCF-7	breast:
21	chr5:179049042..179051273-chr5:179225764..179228331,2	MCF-7	breast:
22	chr5:179047637..179052326-chr5:179245599..179249536,7	K562	blood:
23	chr5:179047831..179051506-chr5:179245810..179250436,9	MCF-7	breast:
24	chr12:108955820..108956766-chr5:179050183..179051036,3	Hela-S3	cervix:
25	chr5:179023314..179026919-chr5:179048927..179051890,4	MCF-7	breast:
26	chr1:53662129..53662856-chr5:179050257..179051236,2	Hela-S3	cervix:
27	chr5:178986094..178988194-chr5:179049451..179052935,4	MCF-7	breast:
28	chr5:179049208..179051645-chr5:179125705..179129690,6	MCF-7	breast:
29	chr15:72523714..72524571-chr5:179050555..179051464,2	Hela-S3	cervix:
30	chr5:179050145..179051089-chr7:128095365..128096266,2	HCT-116	colon:
31	chr5:179048811..179053260-chr5:179101652..179108160,8	MCF-7	breast:
32	chr5:178975871..178983601-chr5:179047224..179052413,15	K562	blood:
33	chr5:179048743..179051829-chr5:179229515..179233744,4	MCF-7	breast:
34	chr12:69079995..69080788-chr5:179050562..179051077,2	Hela-S3	cervix:
35	chr5:178989508..178991362-chr5:179048413..179051335,2	MCF-7	breast:
36	chr5:177630203..177632374-chr5:179049408..179051401,2	MCF-7	breast:
37	chr3:129611962..129612663-chr5:179050573..179051109,2	HCT-116	colon:
38	chr12:7072083..7074369-chr5:179050327..179052683,2	MCF-7	breast:
39	chr5:179048156..179052144-chr5:179103013..179109071,12	K562	blood:
40	chr14:23754854..23755482-chr5:179050344..179050925,2	Hela-S3	cervix:
41	chr17:7387555..7388114-chr5:179050649..179051622,2	Hela-S3	cervix:
42	chr3:182510926..182511584-chr5:179050129..179050994,2	Hela-S3	cervix:
43	chr5:178975440..178984076-chr5:179047224..179053131,17	K562	blood:
44	chr5:179048548..179052839-chr5:179221765..179224480,6	MCF-7	breast:
45	chr5:179049048..179052854-chr5:179122221..179127718,16	MCF-7	breast:
46	chr5:179050662..179051255-chr7:5569791..5570511,2	Hela-S3	cervix:
47	chr13:101327051..101327790-chr5:179050471..179051305,2	NB4	blood:
48	chr5:179050402..179051097-chr7:43965768..43966440,3	Hela-S3	cervix:
49	chr16:87350846..87351666-chr5:179050646..179051491,2	NB4	blood:
50	chr1:178994809..178995971-chr5:179049840..179051236,5	Hela-S3	cervix:

Variant related genes	Relation type
HNRNPH1	TF binding region
ENSG00000006534	Chromatin interaction
ENSG00000119487	Chromatin interaction
ENSG00000172765	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000131876	Chromatin interaction
ENSG00000273184	Chromatin interaction
ENSG00000259215	Chromatin interaction
ENSG00000103932	Chromatin interaction
ENSG00000240063	Chromatin interaction
ENSG00000115241	Chromatin interaction
ENSG00000165182	Chromatin interaction
ENSG00000207708	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000163681	Chromatin interaction
ENSG00000058063	Chromatin interaction
ENSG00000215271	Chromatin interaction
ENSG00000163191	Chromatin interaction
ENSG00000225051	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000264732	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000134717	Chromatin interaction
ENSG00000176783	Chromatin interaction
ENSG00000174579	Chromatin interaction
ENSG00000128016	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000136813	Chromatin interaction
ENSG00000247363	Chromatin interaction
ENSG00000265458	Chromatin interaction
ENSG00000106608	Chromatin interaction
ENSG00000129235	Chromatin interaction
ENSG00000228259	Chromatin interaction
ENSG00000204659	Chromatin interaction
ENSG00000116199	Chromatin interaction
ENSG00000160131	Chromatin interaction
ENSG00000245750	Chromatin interaction
ENSG00000182180	Chromatin interaction
ENSG00000157216	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000174282	Chromatin interaction
ENSG00000078967	Chromatin interaction
ENSG00000270006	Chromatin interaction
ENSG00000227540	Chromatin interaction
ENSG00000250674	Chromatin interaction
ENSG00000216937	Chromatin interaction
ENSG00000271969	Chromatin interaction
ENSG00000136003	Chromatin interaction
ENSG00000197226	Chromatin interaction
ENSG00000126749	Chromatin interaction
ENSG00000141562	Chromatin interaction
ENSG00000173209	Chromatin interaction
ENSG00000198920	Chromatin interaction
ENSG00000240758	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000184831	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000117862	Chromatin interaction
ENSG00000157184	Chromatin interaction
ENSG00000207713	Chromatin interaction
ENSG00000029363	Chromatin interaction
ENSG00000125247	Chromatin interaction
ENSG00000135245	Chromatin interaction
ENSG00000257084	Chromatin interaction
ENSG00000213316	Chromatin interaction
ENSG00000161013	Chromatin interaction
ENSG00000146063	Chromatin interaction
ENSG00000085274	Chromatin interaction
ENSG00000111581	Chromatin interaction
ENSG00000237950	Chromatin interaction
ENSG00000260456	Chromatin interaction
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10076293	0.87[ASN][1000 genomes]
rs1136267	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13162707	0.85[ASN][1000 genomes]
rs28544040	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4078141	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4131080	0.88[ASN][1000 genomes]
rs4376229	0.88[ASN][1000 genomes]
rs6876679	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2829850	chr5:178828854-179060995	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
4	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv883273	chr5:179045142-179086833	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	103 gene(s)	inside rSNPs	diseases
6	nsv823357	chr5:179046318-179058193	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10066669	HNRPH1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179045000-179051200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:179046000-179051200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
3	chr5:179048000-179051800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr5:179048200-179051600	Active TSS	Ovary	ovary
5	chr5:179048400-179051400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:179048600-179051200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:179048800-179051000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:179048800-179051200	Active TSS	Placenta Amnion	Placenta Amnion
9	chr5:179048800-179051400	Active TSS	Lung	lung
10	chr5:179049000-179051000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:179049000-179051000	Active TSS	Adipose Nuclei	Adipose
12	chr5:179049000-179051000	Active TSS	Stomach Smooth Muscle	stomach
13	chr5:179049000-179051200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:179049000-179051200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr5:179049000-179051200	Active TSS	Fetal Muscle Trunk	muscle
16	chr5:179049000-179051200	Active TSS	Pancreas	Pancrea
17	chr5:179049000-179051200	Active TSS	Rectal Smooth Muscle	rectum
18	chr5:179049000-179051200	Active TSS	Right Ventricle	heart
19	chr5:179049000-179051200	Active TSS	Thymus	Thymus
20	chr5:179049000-179051200	Active TSS	NHLF	lung
21	chr5:179049000-179051400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:179049000-179051400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:179049000-179051400	Active TSS	Gastric	stomach
24	chr5:179049000-179051400	Active TSS	Left Ventricle	heart
25	chr5:179049000-179051400	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr5:179049000-179051400	Active TSS	Spleen	Spleen
27	chr5:179049000-179051400	Active TSS	HSMMtube	muscle
28	chr5:179049000-179051600	Active TSS	Aorta	Aorta
29	chr5:179049000-179051600	Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr5:179049000-179051600	Active TSS	Esophagus	oesophagus
31	chr5:179049000-179051600	Active TSS	Psoas Muscle	Psoas
32	chr5:179049000-179051600	Active TSS	Small Intestine	intestine
33	chr5:179049000-179051800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr5:179049200-179051000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr5:179049200-179051000	Active TSS	Cortex derived primary cultured neurospheres	brain
36	chr5:179049200-179051200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:179049200-179051200	Active TSS	Colonic Mucosa	Colon
38	chr5:179049200-179051200	Active TSS	Duodenum Mucosa	Duodenum
39	chr5:179049200-179051200	Active TSS	Fetal Brain Male	brain
40	chr5:179049200-179051200	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr5:179049200-179051200	Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr5:179049200-179051200	Active TSS	NHEK	skin
43	chr5:179049200-179051600	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr5:179049200-179051600	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr5:179049200-179051600	Active TSS	Liver	Liver
46	chr5:179049200-179051600	Active TSS	Brain Anterior Caudate	brain
47	chr5:179049200-179051600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:179049200-179051600	Active TSS	Brain Substantia Nigra	brain
49	chr5:179049200-179051600	Active TSS	Colon Smooth Muscle	Colon
50	chr5:179049200-179051600	Active TSS	Stomach Mucosa	stomach

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