Variant report

Variant	rs71423566
Chromosome Location	chr2:179345183-179345184
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	TAF1	chr2:179345089-179345351	GM12891	blood:	n/a	n/a
2	POLR2A	chr2:179344674-179345433	U87	brain:	n/a	n/a
3	TFAP2A	chr2:179344671-179345345	Hela-S3	cervix:	n/a	chr2:179345092-179345102 chr2:179344946-179344958 chr2:179345112-179345127 chr2:179345110-179345122 chr2:179345092-179345102 chr2:179344946-179344958 chr2:179345092-179345102 chr2:179344946-179344958
4	POU2F2	chr2:179345124-179345311	GM12878	blood:	n/a	n/a
5	SIN3AK20	chr2:179344884-179345482	HepG2	liver:	n/a	n/a
6	REST	chr2:179344442-179346116	H1-neurons	neurons:	n/a	chr2:179345081-179345094 chr2:179345406-179345419 chr2:179345673-179345683
7	TAF1	chr2:179345120-179345359	GM12891	blood:	n/a	n/a
8	ELF1	chr2:179344840-179345495	GM12878	blood:	n/a	chr2:179345142-179345151 chr2:179345347-179345359 chr2:179345184-179345195 chr2:179345351-179345360
9	POLR2A	chr2:179344742-179345464	PFSK-1	brain:	n/a	n/a
10	ETS1	chr2:179344833-179345486	K562	blood:	n/a	chr2:179345187-179345198 chr2:179345139-179345150
11	TAF1	chr2:179344704-179345393	ECC-1	luminal epithelium:	n/a	n/a
12	MAX	chr2:179344666-179345409	HepG2	liver:	n/a	n/a
13	MXI1	chr2:179344702-179345521	GM12878	blood:	n/a	n/a
14	STAT1	chr2:179344955-179345200	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:179344790-179345471	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr2:179344712-179345396	H1-neurons	neurons:	n/a	n/a
17	HNF4A	chr2:179344781-179345247	HepG2	liver:	n/a	chr2:179345202-179345218 chr2:179345207-179345214
18	RUNX3	chr2:179344798-179345262	GM12878	blood:	n/a	n/a
19	E2F6	chr2:179344868-179345196	K562	blood:	n/a	chr2:179345121-179345130 chr2:179345139-179345148 chr2:179345140-179345150
20	ELF1	chr2:179344784-179345424	HepG2	liver:	n/a	chr2:179345142-179345151 chr2:179345347-179345359 chr2:179345184-179345195 chr2:179345351-179345360
21	MYC	chr2:179344835-179345952	A549	lung:	n/a	chr2:179345670-179345680
22	POLR2A	chr2:179344828-179345499	HepG2	liver:	n/a	n/a
23	NR2C2	chr2:179344985-179345362	HepG2	liver:	n/a	n/a
24	TBP	chr2:179345128-179345328	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr2:179344818-179345767	GM12891	blood:	n/a	n/a
26	ZBTB7A	chr2:179344773-179345308	K562	blood:	n/a	n/a
27	POLR2A	chr2:179344804-179345369	HepG2	liver:	n/a	n/a
28	CREB1	chr2:179344907-179345288	A549	lung:	n/a	n/a
29	ELF1	chr2:179344856-179345532	MCF-7	breast:	n/a	chr2:179345142-179345151 chr2:179345347-179345359 chr2:179345184-179345195 chr2:179345351-179345360
30	TAF1	chr2:179344821-179345605	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:179344880-179345883	PBDE	blood:	n/a	n/a
32	POLR2A	chr2:179344870-179345529	HUVEC	blood vessel:	n/a	n/a
33	CREB1	chr2:179344782-179345643	A549	lung:	n/a	n/a
34	POLR2A	chr2:179344813-179345585	HUVEC	blood vessel:	n/a	n/a
35	CTCF	chr2:179345018-179345331	Spleen_OC	spleen:	n/a	chr2:179345274-179345287 chr2:179345306-179345319
36	PBX3	chr2:179344797-179345403	SK-N-SH	brain:	n/a	n/a
37	TCF7L2	chr2:179344751-179345363	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr2:179344882-179345487	GM12878	blood:	n/a	n/a
39	HDAC2	chr2:179344921-179345347	H1-hESC	embryonic stem cell:	n/a	n/a
40	MAX	chr2:179344778-179345287	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr2:179344786-179345954	GM12892	blood:	n/a	n/a
42	HNF4G	chr2:179344785-179345292	HepG2	liver:	n/a	chr2:179345202-179345218 chr2:179345207-179345214
43	STAT3	chr2:179344989-179345234	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr2:179344662-179346225	MCF10A-Er-Src	breast:	n/a	n/a
45	TAF1	chr2:179344969-179345317	Hela-S3	cervix:	n/a	n/a
46	RCOR1	chr2:179344793-179345981	K562	blood:	n/a	n/a
47	TCF7L2	chr2:179344866-179345671	HCT-116	colon:	n/a	n/a
48	NRF1	chr2:179344516-179346022	SK-N-SH	brain:	n/a	chr2:179345121-179345130 chr2:179345086-179345097 chr2:179345068-179345079
49	SIN3AK20	chr2:179344797-179345350	HepG2	liver:	n/a	n/a
50	POLR2A	chr2:179344814-179346003	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:179345168-179345218	MCF-7	breast:	n/a
2	chr2:179345173-179345223	HUVEC	blood vessel:	n/a
3	chr2:179345168-179345218	AG09319	gingival:	n/a
4	chr2:179345168-179345218	HRE	kidney:	n/a
5	chr2:179345168-179345218	AG09309	skin:	n/a
6	chr2:179345173-179345223	K562	blood:	n/a
7	chr2:179345173-179345223	NB4	blood:	n/a
8	chr2:179345168-179345218	K562	blood:	n/a
9	chr2:179345173-179345223	HEK293	kidney:	embryo
10	chr2:179345173-179345223	MCF-7	breast:	n/a
11	chr2:179345168-179345218	SKMC	muscle:	n/a
12	chr2:179345173-179345223	HIPEpiC	eye:	n/a
13	chr2:179345168-179345218	RPTEC	kidney:	n/a
14	chr2:179345168-179345218	NHDF-neo	bronchial:	n/a
15	chr2:179345173-179345223	SAEC	small airway:	n/a
16	chr2:179345173-179345223	Hepatocyte	liver:	n/a
17	chr2:179345173-179345223	HCM	heart:	n/a
18	chr2:179345173-179345223	RPTEC	kidney:	n/a
19	chr2:179345168-179345218	HRPEpiC	eye:	n/a
20	chr2:179345168-179345218	Jurkat	blood:	n/a
21	chr2:179345168-179345218	T-47D	breast:	n/a
22	chr2:179345168-179345218	BE2_C	brain:	n/a
23	chr2:179345173-179345223	IMR90	lung:	fetal
24	chr2:179345168-179345218	HUVEC	blood vessel:	n/a
25	chr2:179345168-179345218	HMEC	breast:	n/a
26	chr2:179345173-179345223	BE2_C	brain:	n/a
27	chr2:179345173-179345223	HMEC	breast:	n/a
28	chr2:179345173-179345223	HCT-116	colon:	n/a
29	chr2:179345173-179345223	HEEpiC	esophagus:	n/a
30	chr2:179345173-179345223	ProgFib	skin:	n/a
31	chr2:179345173-179345223	HepG2	liver:	n/a
32	chr2:179345173-179345223	AG09309	skin:	n/a
33	chr2:179345173-179345223	HL-60	blood:	n/a
34	chr2:179345173-179345223	NHDF-neo	bronchial:	n/a
35	chr2:179345168-179345218	HEK293	kidney:	embryo
36	chr2:179345168-179345218	SK-N-SH	brain:	n/a
37	chr2:179345168-179345218	SK-N-SH_RA	brain:	n/a
38	chr2:179345168-179345218	MCF10A-Er-Src	breast:	n/a
39	chr2:179345173-179345223	AG09319	gingival:	n/a
40	chr2:179345173-179345223	GM12892	blood:	n/a
41	chr2:179345168-179345218	ovcar-3	ovarian:	n/a
42	chr2:179345168-179345218	HNPCEpiC	eye:	n/a
43	chr2:179345168-179345218	HRCEpiC	kidney:	n/a
44	chr2:179345173-179345223	HAEpiC	amniotic membrane:	n/a
45	chr2:179345173-179345223	CMK	blood:	n/a
46	chr2:179345168-179345218	LNCaP	prostate:	n/a
47	chr2:179345168-179345218	U87	brain:	n/a
48	chr2:179345168-179345218	SAEC	small airway:	n/a
49	chr2:179345173-179345223	SK-N-MC	brain:	n/a
50	chr2:179345168-179345218	HCM	heart:	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:74034038..74036346-chr2:179345014..179347619,2	MCF-7	breast:
2	chr2:179277322..179281063-chr2:179341771..179345640,5	K562	blood:
3	chr2:179309273..179312087-chr2:179344521..179346573,2	MCF-7	breast:
4	chr2:179312045..179317660-chr2:179337933..179347437,24	MCF-7	breast:
5	chr2:179319205..179322423-chr2:179341743..179345832,4	K562	blood:
6	chr2:179310863..179318324-chr2:179338966..179346608,29	K562	blood:
7	chr2:179343391..179346043-chr2:179387218..179389955,4	K562	blood:
8	chr2:178128296..178129936-chr2:179344780..179347369,2	MCF-7	breast:
9	chr17:78120561..78121271-chr2:179344416..179345189,2	HCT-116	colon:
10	chr2:179314444..179318442-chr2:179340876..179346721,19	MCF-7	breast:
11	chr2:179311363..179318324-chr2:179340414..179346232,28	K562	blood:
12	chr2:179344389..179346577-chr2:179386170..179387840,3	K562	blood:

Variant related genes	Relation type
PLEKHA3	TF binding region
FKBP7	TF binding region
FKBP7	CpG island
PLEKHA3	CpG island
ENSG00000180228	Chromatin interaction
ENSG00000116044	Chromatin interaction
ENSG00000204311	Chromatin interaction
ENSG00000222043	Chromatin interaction
ENSG00000223960	Chromatin interaction
ENSG00000237298	Chromatin interaction
ENSG00000269926	Chromatin interaction
ENSG00000238082	Chromatin interaction
ENSG00000141543	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs13026251	0.84[AMR][1000 genomes]
rs3820979	0.84[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs71423566	RP11-171I2.2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179341200-179346000	Active TSS	Fetal Brain Female	brain
2	chr2:179341800-179345600	Active TSS	Brain Germinal Matrix	brain
3	chr2:179341800-179345800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:179342000-179346200	Active TSS	Fetal Kidney	kidney
5	chr2:179342000-179346400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:179342000-179346400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:179342000-179346600	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr2:179342200-179345800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:179342200-179347200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr2:179342400-179346200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr2:179342400-179346200	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr2:179342400-179346200	Active TSS	Psoas Muscle	Psoas
13	chr2:179342400-179346200	Active TSS	HSMM	muscle
14	chr2:179342400-179346600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:179342400-179347000	Active TSS	HSMMtube	muscle
16	chr2:179342600-179345800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr2:179342600-179345800	Active TSS	Thymus	Thymus
18	chr2:179342600-179346000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr2:179342600-179346200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:179342600-179346200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:179342600-179346400	Active TSS	Right Ventricle	heart
22	chr2:179342600-179346600	Active TSS	Aorta	Aorta
23	chr2:179342600-179346600	Active TSS	Brain Angular Gyrus	brain
24	chr2:179342600-179347000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:179342800-179345800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr2:179342800-179347000	Active TSS	Left Ventricle	heart
27	chr2:179343600-179345200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
28	chr2:179344000-179345200	Weak transcription	Gastric	stomach
29	chr2:179344000-179345200	Weak transcription	Lung	lung
30	chr2:179344000-179345200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr2:179344000-179346200	Active TSS	Right Atrium	heart
32	chr2:179344400-179345800	Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr2:179344600-179345200	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr2:179344600-179345800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr2:179344600-179346000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:179344600-179346000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:179344600-179346000	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:179344600-179346000	Active TSS	Small Intestine	intestine
39	chr2:179344600-179346200	Active TSS	Brain Hippocampus Middle	brain
40	chr2:179344600-179346200	Active TSS	Colonic Mucosa	Colon
41	chr2:179344600-179346200	Active TSS	Placenta Amnion	Placenta Amnion
42	chr2:179344600-179346600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr2:179344800-179345800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:179344800-179345800	Active TSS	Primary T cells from cord blood	blood
45	chr2:179344800-179345800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:179344800-179345800	Active TSS	Brain Cingulate Gyrus	brain
47	chr2:179344800-179345800	Active TSS	Brain Substantia Nigra	brain
48	chr2:179344800-179345800	Weak transcription	Fetal Heart	heart
49	chr2:179344800-179345800	Active TSS	Fetal Lung	lung
50	chr2:179344800-179345800	Active TSS	Skeletal Muscle Female	skeletal muscle

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