Variant report

Variant	rs7757549
Chromosome Location	chr6:166744262-166744263
allele	C/G
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	NFYB	chr6:166744057-166744520	K562	blood:	n/a	chr6:166744278-166744293 chr6:166744279-166744293 chr6:166744281-166744291 chr6:166744278-166744293
2	POLR2A	chr6:166743896-166744608	GM12878	blood:	n/a	n/a
3	YY1	chr6:166744160-166744441	K562	blood:	n/a	n/a
4	POLR2A	chr6:166744044-166744362	H1-hESC	embryonic stem cell:	n/a	n/a
5	NFIC	chr6:166744050-166744513	SK-N-SH	brain:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
6	SP1	chr6:166744070-166744513	H1-hESC	embryonic stem cell:	n/a	chr6:166744303-166744313 chr6:166744298-166744308 chr6:166744271-166744292 chr6:166744297-166744308 chr6:166744450-166744464
7	MYC	chr6:166744045-166744537	K562	blood:	n/a	n/a
8	RAD21	chr6:166744068-166744522	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
9	RAD21	chr6:166744096-166744466	SK-N-SH_RA	brain:	n/a	chr6:166744291-166744304
10	CTCF	chr6:166744240-166744390	HRPEpiC	eye:	n/a	n/a
11	POLR2A	chr6:166743901-166744593	H1-hESC	embryonic stem cell:	n/a	n/a
12	HCFC1	chr6:166744087-166744539	K562	blood:	n/a	n/a
13	SMC3	chr6:166743979-166744580	HepG2	liver:	n/a	n/a
14	ARID3A	chr6:166744117-166744850	HepG2	liver:	n/a	n/a
15	RFX5	chr6:166744162-166744418	HepG2	liver:	n/a	n/a
16	CTCF	chr6:166744240-166744390	HPF	lung:	n/a	n/a
17	MXI1	chr6:166743827-166744730	SK-N-SH	brain:	n/a	n/a
18	TEAD4	chr6:166743945-166744638	HepG2	liver:	n/a	n/a
19	GTF2F1	chr6:166744130-166744330	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr6:166744030-166744549	GM12878	blood:	n/a	n/a
21	ELF1	chr6:166744192-166744413	K562	blood:	n/a	n/a
22	NFIC	chr6:166743973-166744658	SK-N-SH	brain:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
23	RCOR1	chr6:166744060-166744464	HepG2	liver:	n/a	n/a
24	RAD21	chr6:166744145-166744529	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
25	NFIC	chr6:166743950-166744652	ECC-1	luminal epithelium:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
26	CTCF	chr6:166744260-166744410	A549	lung:	n/a	n/a
27	CTCF	chr6:166744220-166744370	SAEC	small airway:	n/a	chr6:166744232-166744245
28	SP4	chr6:166744110-166744546	H1-hESC	embryonic stem cell:	n/a	chr6:166744297-166744308
29	CTCF	chr6:166744240-166744390	BE2_C	brain:	n/a	n/a
30	TBL1XR1	chr6:166744122-166745211	K562	blood:	n/a	n/a
31	CTCF	chr6:166744260-166744410	NHLF	lung:	n/a	n/a
32	POLR2A	chr6:166744051-166744482	HepG2	liver:	n/a	n/a
33	RAD21	chr6:166744156-166744433	SK-N-SH_RA	brain:	n/a	chr6:166744291-166744304
34	CTCF	chr6:166743971-166744560	K562	blood:	n/a	chr6:166744232-166744245
35	USF1	chr6:166744139-166744465	K562	blood:	n/a	n/a
36	TAF1	chr6:166744069-166744344	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:166744196-166744413	SK-N-SH_RA	brain:	n/a	chr6:166744232-166744245
38	MAX	chr6:166744180-166744564	HepG2	liver:	n/a	n/a
39	POLR2A	chr6:166744067-166744456	H1-hESC	embryonic stem cell:	n/a	n/a
40	RAD21	chr6:166744031-166744589	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
41	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a
42	POLR2A	chr6:166743983-166744597	GM12892	blood:	n/a	n/a
43	TAF1	chr6:166744043-166744541	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:166744040-166744527	GM12891	blood:	n/a	n/a
45	CTCF	chr6:166744220-166744370	HAc	cerebellar:	n/a	chr6:166744232-166744245
46	HDAC2	chr6:166744082-166744462	H1-hESC	embryonic stem cell:	n/a	n/a
47	UBTF	chr6:166744066-166744521	K562	blood:	n/a	n/a
48	ARID3A	chr6:166743832-166744548	K562	blood:	n/a	n/a
49	CTCF	chr6:166744183-166744508	GM12878	blood:	n/a	chr6:166744232-166744245
50	YY1	chr6:166743999-166744412	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:166743880..166744818-chr6:166814023..166814944,3	K562	blood:
2	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
3	chr6:166689019..166690684-chr6:166742246..166744543,2	K562	blood:
4	chr6:166743853..166744743-chr6:166794927..166795865,3	K562	blood:
5	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
6	chr6:166744077..166744772-chr6:166795075..166795860,2	MCF-7	breast:

Variant related genes	Relation type
HNRNPA1P49	TF binding region
SFT2D1	TF binding region
ENSG00000261420	Chromatin interaction
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10806847	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2343590	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4470829	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4598048	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4709112	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6909951	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6918901	0.99[EUR][1000 genomes]
rs6927168	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355572	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9356476	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356478	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356479	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9366005	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366006	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366007	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9459654	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7757549	HNRNPA1P49	cis	lung	GTEx
rs7757549	SFT2D1	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:166733200-166744400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
6	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
7	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
8	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
9	chr6:166737000-166745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr6:166738200-166754200	Weak transcription	NH-A	brain
11	chr6:166739400-166744400	Weak transcription	Brain Angular Gyrus	brain
12	chr6:166739400-166745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:166739400-166748000	Weak transcription	Gastric	stomach
15	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
17	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
18	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:166741400-166750000	Weak transcription	HMEC	breast
20	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:166742200-166744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr6:166742400-166744400	Weak transcription	Colon Smooth Muscle	Colon
26	chr6:166742400-166744800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:166742600-166745600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:166742600-166746200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:166742600-166746400	Weak transcription	Placenta	Placenta
31	chr6:166742600-166746400	Weak transcription	Lung	lung
32	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
33	chr6:166742800-166744400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:166742800-166745200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:166742800-166745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr6:166742800-166745800	Weak transcription	Spleen	Spleen
37	chr6:166742800-166746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:166742800-166746200	Weak transcription	Fetal Intestine Small	intestine
39	chr6:166742800-166746200	Weak transcription	Osteobl	bone
40	chr6:166742800-166746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr6:166742800-166746400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:166742800-166746400	Weak transcription	Aorta	Aorta
43	chr6:166742800-166746400	Weak transcription	Fetal Muscle Leg	muscle
44	chr6:166742800-166746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr6:166742800-166746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:166742800-166747000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:166742800-166748400	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr6:166742800-166749200	Weak transcription	NHEK	skin
49	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
50	chr6:166742800-166751000	Weak transcription	HSMM	muscle

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