Variant report

Variant	rs10455976
Chromosome Location	chr6:166748622-166748623
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:32)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:32 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:166746252-166749844	GM12891	blood:	n/a	n/a
2	BATF	chr6:166748460-166748786	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:166747895-166748701	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:166746318-166748671	HL-60	blood:	n/a	n/a
5	POLR2A	chr6:166747027-166748876	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:166746571-166749863	GM12892	blood:	n/a	n/a
7	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a
8	POLR2A	chr6:166746147-166749873	GM12891	blood:	n/a	n/a
9	POLR2A	chr6:166746274-166749904	GM12891	blood:	n/a	n/a
10	POLR2A	chr6:166748232-166748789	K562	blood:	n/a	n/a
11	POLR2A	chr6:166746206-166754614	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:166745653-166751514	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:166748138-166748859	IMR90	lung:	n/a	n/a
14	NFATC1	chr6:166746279-166748938	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:166745484-166754512	GM12892	blood:	n/a	n/a
16	POLR2A	chr6:166748439-166748706	K562	blood:	n/a	n/a
17	POLR2A	chr6:166747886-166748929	K562	blood:	n/a	n/a
18	POLR2A	chr6:166745570-166751783	GM12892	blood:	n/a	n/a
19	POLR2A	chr6:166747421-166748641	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr6:166746365-166757465	GM12878	blood:	n/a	n/a
21	POLR2A	chr6:166747865-166748849	K562	blood:	n/a	n/a
22	POLR2A	chr6:166748370-166748748	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:166745466-166757224	GM12878	blood:	n/a	n/a
24	NFATC1	chr6:166748037-166748947	GM12878	blood:	n/a	n/a
25	POLR2A	chr6:166745668-166754554	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:166748404-166748817	GM12878	blood:	n/a	n/a
27	POLR2A	chr6:166747539-166748890	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr6:166745300-166754633	GM12891	blood:	n/a	n/a
29	POLR2A	chr6:166748396-166749078	HepG2	liver:	n/a	n/a
30	MTA3	chr6:166746591-166750124	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:166748079-166748709	HepG2	liver:	n/a	n/a
32	POLR2A	chr6:166747648-166748914	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:166748234..166750279-chr6:166754280..166756518,2	MCF-7	breast:
2	chr6:166748322..166751240-chr6:166751244..166753150,2	MCF-7	breast:
3	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10455809	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10455977	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10455978	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10946152	0.83[EUR][1000 genomes]
rs10946158	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10946160	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10946161	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11551053	0.89[ASN][1000 genomes]
rs11752886	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11753652	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11755305	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12198613	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209616	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12214281	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12214812	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12662924	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1599841	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2294333	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294334	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294335	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4144886	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4144887	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4144888	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55936781	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59337176	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66461381	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs68016351	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73030701	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73263155	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73788236	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7753161	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7767887	0.84[ASN][1000 genomes]
rs7771603	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs941683	0.93[EUR][1000 genomes];0.96[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	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
2	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
3	nsv981205	chr6:166748596-166751156	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10455976	SFT2D1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
3	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
4	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
5	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
6	chr6:166738200-166754200	Weak transcription	NH-A	brain
7	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
9	chr6:166741400-166750000	Weak transcription	HMEC	breast
10	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
13	chr6:166742800-166749200	Weak transcription	NHEK	skin
14	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
15	chr6:166742800-166751000	Weak transcription	HSMM	muscle
16	chr6:166743000-166749200	Weak transcription	Fetal Lung	lung
17	chr6:166743000-166749600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr6:166743400-166749600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:166744400-166750600	Weak transcription	NHLF	lung
20	chr6:166744400-166752000	Weak transcription	Right Atrium	heart
21	chr6:166744400-166754800	Weak transcription	NHDF-Ad	bronchial
22	chr6:166744600-166750400	Weak transcription	Ovary	ovary
23	chr6:166744800-166749400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:166745200-166749400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr6:166745200-166750400	Weak transcription	Stomach Mucosa	stomach
26	chr6:166745400-166754400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr6:166745400-166755000	Weak transcription	A549	lung
28	chr6:166745600-166749000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:166745600-166749200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:166745800-166748800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:166745800-166749200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:166745800-166749800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr6:166745800-166752200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:166746000-166752000	Strong transcription	Fetal Intestine Large	intestine
35	chr6:166746200-166752800	Strong transcription	Fetal Intestine Small	intestine
36	chr6:166746200-166753800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr6:166746200-166754800	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr6:166746400-166749800	Genic enhancers	Thymus	Thymus
39	chr6:166746400-166752600	Genic enhancers	Spleen	Spleen
40	chr6:166746600-166749200	Weak transcription	Brain Angular Gyrus	brain
41	chr6:166746600-166750400	Weak transcription	Brain Anterior Caudate	brain
42	chr6:166746600-166751800	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:166746600-166752400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:166746800-166749000	Weak transcription	Fetal Brain Female	brain
45	chr6:166747000-166750000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr6:166747000-166750000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:166747000-166750400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:166747000-166753400	Weak transcription	Fetal Brain Male	brain
49	chr6:166747200-166749200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr6:166747200-166750000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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