Variant report

Variant	rs860699
Chromosome Location	chr12:50451102-50451103
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	CTCF	chr12:50451080-50451230	NHEK	skin:	n/a	n/a
2	CTCF	chr12:50450823-50451151	GM19239	blood:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
3	CTCF	chr12:50450960-50451110	AG04450	lung:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
4	CTCF	chr12:50450987-50451170	NHEK	skin:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
5	CTCF	chr12:50450940-50451230	GM12873	blood:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
6	CTCF	chr12:50451053-50451173	MCF-7	breast:	n/a	chr12:50451060-50451073
7	CTCF	chr12:50451040-50451190	HepG2	liver:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
8	TAF1	chr12:50450853-50451544	H1-neurons	neurons:	n/a	n/a
9	MAZ	chr12:50451096-50451295	HepG2	liver:	n/a	n/a
10	CTCF	chr12:50451032-50451508	K562	blood:	n/a	chr12:50451041-50451050 chr12:50451252-50451265 chr12:50451391-50451404 chr12:50451060-50451073
11	CTCF	chr12:50451040-50451190	AG10803	skin:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
12	FOXP2	chr12:50450905-50451544	PFSK-1	brain:	n/a	n/a
13	CEBPD	chr12:50451030-50451274	HepG2	liver:	n/a	n/a
14	CTCF	chr12:50450860-50451150	WI-38	lung:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
15	CTCF	chr12:50450960-50451110	WERI-Rb-1	eye:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
16	POLR2A	chr12:50450888-50451212	HepG2	liver:	n/a	n/a
17	CTCF	chr12:50451020-50451170	GM12873	blood:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
18	CTCF	chr12:50451040-50451190	GM12870	blood:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
19	NRF1	chr12:50450793-50451689	SK-N-SH	brain:	n/a	chr12:50451353-50451367 chr12:50451356-50451370 chr12:50451356-50451365 chr12:50451356-50451367 chr12:50451309-50451318
20	MAZ	chr12:50451064-50451655	K562	blood:	n/a	chr12:50451390-50451400
21	POLR2A	chr12:50451002-50451559	HCT-116	colon:	n/a	n/a
22	MXI1	chr12:50450578-50451858	IMR90	lung:	n/a	n/a
23	RCOR1	chr12:50450978-50451461	Hela-S3	cervix:	n/a	n/a
24	MYC	chr12:50451014-50451120	MCF-7	breast:	n/a	n/a
25	CTCF	chr12:50451060-50451210	SK-N-SH_RA	brain:	n/a	chr12:50451060-50451073
26	CTCF	chr12:50451080-50451230	HPAF	blood vessel:	n/a	n/a
27	CTBP2	chr12:50449663-50451559	H1-hESC	embryonic stem cell:	n/a	n/a
28	MYC	chr12:50450694-50451557	NB4	blood:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
29	MAX	chr12:50450478-50451662	MCF-7	breast:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
30	POLR2A	chr12:50450980-50451152	Gliobla	brain:	n/a	n/a
31	CTCF	chr12:50451000-50451150	WERI-Rb-1	eye:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
32	CTCF	chr12:50449519-50451803	A549	lung:	n/a	chr12:50449938-50449956 chr12:50451041-50451050 chr12:50451664-50451677 chr12:50449933-50449954 chr12:50451252-50451265 chr12:50451667-50451680 chr12:50451391-50451404 chr12:50451060-50451073
33	MAX	chr12:50450831-50451582	SK-N-SH	brain:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
34	POLR2A	chr12:50451074-50451454	MCF-7	breast:	n/a	n/a
35	MAX	chr12:50450488-50451529	H1-hESC	embryonic stem cell:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
36	UBTF	chr12:50451097-50451683	K562	blood:	n/a	n/a
37	SMC3	chr12:50450869-50451484	Hela-S3	cervix:	n/a	n/a
38	TAF1	chr12:50451001-50451718	ECC-1	luminal epithelium:	n/a	n/a
39	CTCF	chr12:50451000-50451150	GM12864	blood:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
40	POLR2A	chr12:50450794-50451635	H1-neurons	neurons:	n/a	n/a
41	FOXA1	chr12:50450892-50451176	T-47D	breast:	n/a	n/a
42	MYC	chr12:50450986-50451221	MCF-7	breast:	n/a	n/a
43	E2F6	chr12:50450975-50451569	A549	lung:	n/a	chr12:50451268-50451277 chr12:50451357-50451366 chr12:50451386-50451398
44	MAX	chr12:50450533-50451609	H1-hESC	embryonic stem cell:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
45	MAX	chr12:50450534-50451748	A549	lung:	n/a	chr12:50451390-50451400 chr12:50450863-50450873
46	POLR2A	chr12:50450697-50451673	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr12:50451022-50451452	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr12:50451040-50451190	AG04449	skin:	n/a	chr12:50451041-50451050 chr12:50451060-50451073
49	ZBTB7A	chr12:50450967-50452040	ECC-1	luminal epithelium:	n/a	n/a
50	PAX5	chr12:50450766-50451139	GM12878	blood:	n/a	chr12:50450979-50450998 chr12:50450980-50450998 chr12:50450982-50450999

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:50451095-50451145	HCT-116	colon:	n/a
2	chr12:50451095-50451145	HNPCEpiC	eye:	n/a
3	chr12:50451095-50451145	NHDF-neo	bronchial:	n/a
4	chr12:50451095-50451145	GM06990	blood:	n/a
5	chr12:50451095-50451145	GM12891	blood:	n/a
6	chr12:50451095-50451145	SK-N-SH	brain:	n/a
7	chr12:50451095-50451145	RPTEC	kidney:	n/a
8	chr12:50451095-50451145	Caco-2	colon:	n/a
9	chr12:50451095-50451145	HepG2	liver:	n/a
10	chr12:50451095-50451145	PANC-1	pancreas:	n/a
11	chr12:50451095-50451145	MCF-7	breast:	n/a
12	chr12:50451095-50451145	ECC-1	luminal epithelium:	n/a
13	chr12:50451095-50451145	SKMC	muscle:	n/a
14	chr12:50451095-50451145	HRPEpiC	eye:	n/a
15	chr12:50451095-50451145	PFSK-1	brain:	n/a
16	chr12:50451095-50451145	NHBE	bronchial:	n/a
17	chr12:50451095-50451145	HEEpiC	esophagus:	n/a
18	chr12:50451095-50451145	GM12892	blood:	n/a
19	chr12:50451095-50451145	BJ	skin:	n/a
20	chr12:50451095-50451145	NB4	blood:	n/a
21	chr12:50451095-50451145	HRE	kidney:	n/a
22	chr12:50451095-50451145	NH-A	brain:	n/a
23	chr12:50451095-50451145	Hela-S3	cervix:	n/a
24	chr12:50451095-50451145	HRCEpiC	kidney:	n/a
25	chr12:50451095-50451145	LNCaP	prostate:	n/a
26	chr12:50451095-50451145	AG04450	lung:	fetal
27	chr12:50451095-50451145	HCPEpiC	choroid plexus:	n/a
28	chr12:50451095-50451145	GM19239	blood:	n/a
29	chr12:50451095-50451145	HCM	heart:	n/a
30	chr12:50451095-50451145	HEK293	kidney:	embryo
31	chr12:50451095-50451145	ovcar-3	ovarian:	n/a
32	chr12:50451095-50451145	SAEC	small airway:	n/a
33	chr12:50451095-50451145	AG04449	skin:	fetal
34	chr12:50451095-50451145	HMEC	breast:	n/a
35	chr12:50451095-50451145	IMR90	lung:	fetal
36	chr12:50451095-50451145	Jurkat	blood:	n/a
37	chr12:50451095-50451145	NT2-D1	testis:	n/a
38	chr12:50451095-50451145	Hepatocyte	liver:	n/a
39	chr12:50451095-50451145	HUVEC	blood vessel:	n/a
40	chr12:50451095-50451145	BE2_C	brain:	n/a
41	chr12:50451095-50451145	CMK	blood:	n/a
42	chr12:50451095-50451145	ProgFib	skin:	n/a
43	chr12:50451095-50451145	T-47D	breast:	n/a
44	chr12:50451095-50451145	AG09319	gingival:	n/a
45	chr12:50451095-50451145	HPAEpiC	pulmonary alveolar:	n/a
46	chr12:50451095-50451145	SK-N-SH_RA	brain:	n/a
47	chr12:50451095-50451145	HL-60	blood:	n/a
48	chr12:50451095-50451145	H1-hESC	embryonic stem cell:	embryo
49	chr12:50451095-50451145	MCF10A-Er-Src	breast:	n/a
50	chr12:50451095-50451145	AoSMC	blood vessel:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
2	chr12:50450859..50453547-chr12:50463168..50465511,2	MCF-7	breast:
3	chr12:50450302..50454051-chr12:50467339..50469182,3	K562	blood:
4	chr12:50260849..50261466-chr12:50450404..50451185,2	K562	blood:
5	chr12:50358701..50362803-chr12:50449341..50451682,4	MCF-7	breast:
6	chr12:50417982..50420791-chr12:50450221..50452010,2	MCF-7	breast:
7	chr12:50360514..50361964-chr12:50449435..50451127,13	K562	blood:
8	chr12:50449658..50451557-chr12:50467280..50470251,2	MCF-7	breast:
9	chr12:50449562..50451220-chr12:50537075..50538581,2	K562	blood:

Variant related genes	Relation type
ASIC1	TF binding region
ASIC1	CpG island
ENSG00000110881	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000161800	Chromatin interaction
ENSG00000086159	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs376184	0.85[ASN][1000 genomes]
rs386469	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393848	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs404751	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs439171	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450423	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs484951	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs590460	0.92[ASN][1000 genomes]
rs613066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627869	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs627887	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs685012	0.80[ASN][1000 genomes]
rs706789	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs706794	0.85[ASN][1000 genomes]
rs835591	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs835593	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs835594	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs836184	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs836185	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs836186	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844359	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv558840	chr12:50449976-50523964	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50449600-50451200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
2	chr12:50449600-50451200	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
3	chr12:50449600-50451200	Flanking Active TSS	Brain Anterior Caudate	brain
4	chr12:50449600-50451200	Flanking Active TSS	Brain Germinal Matrix	brain
5	chr12:50449600-50452200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:50449800-50451400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:50449800-50452000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr12:50450200-50451400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr12:50450400-50451200	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:50450400-50451200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
11	chr12:50450400-50451200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr12:50450400-50451200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
13	chr12:50450400-50451200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
14	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
15	chr12:50450600-50451200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:50450600-50451200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
21	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
22	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Primary T killer memory cells from peripheral blood	blood
23	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
25	chr12:50450600-50451200	Flanking Active TSS	Fetal Heart	heart
26	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
27	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
28	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
29	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr12:50450600-50451200	Flanking Active TSS	Pancreas	Pancrea
31	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
32	chr12:50450600-50451200	Flanking Active TSS	Right Ventricle	heart
33	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Dnd41	blood
34	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	NHEK	skin
35	chr12:50450600-50451200	Flanking Bivalent TSS/Enh	Osteobl	bone
36	chr12:50450600-50451400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr12:50450600-50451400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:50450600-50451400	Flanking Active TSS	Fetal Brain Male	brain
39	chr12:50450600-50451800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
40	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:50450800-50451200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:50450800-50451200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:50450800-50451200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
45	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
46	chr12:50450800-50451200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
48	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
49	chr12:50450800-50451200	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:50450800-50451200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood

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