Variant report

Variant	rs12219064
Chromosome Location	chr10:99332223-99332224
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	CTCF	chr10:99332120-99332270	AoAF	blood vessel:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
2	CEBPB	chr10:99332008-99332439	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr10:99332001-99332344	GM12878	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
4	ELF1	chr10:99331927-99332448	GM12878	blood:	n/a	n/a
5	CCNT2	chr10:99331935-99332286	K562	blood:	n/a	n/a
6	CTCF	chr10:99331897-99332409	H1-hESC	embryonic stem cell:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
7	CTCF	chr10:99332039-99332296	GM10266	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
8	GABPA	chr10:99331937-99332352	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr10:99332080-99332319	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr10:99332220-99332370	A549	lung:	n/a	n/a
11	RAD21	chr10:99331916-99332388	HepG2	liver:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
12	CTCF	chr10:99332100-99332250	GM12878	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
13	CEBPB	chr10:99332074-99332321	HepG2	liver:	n/a	n/a
14	CTCF	chr10:99332021-99332325	MCF-7	breast:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
15	CTCF	chr10:99331866-99332346	GM19238	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
16	POLR2A	chr10:99332036-99332350	HCT-116	colon:	n/a	n/a
17	RAD21	chr10:99332055-99332369	GM12878	blood:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
18	CTCF	chr10:99332160-99332310	HAc	cerebellar:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
19	JUND	chr10:99331997-99332371	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr10:99332100-99332250	GM12874	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
21	TCF12	chr10:99331350-99332874	ECC-1	luminal epithelium:	n/a	chr10:99331620-99331627
22	CEBPB	chr10:99332016-99332428	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr10:99332080-99332230	GM12874	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
24	CTCF	chr10:99332035-99332339	Medullo	brain:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
25	CTCF	chr10:99331468-99332640	A549	lung:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
26	GTF2F1	chr10:99332041-99332329	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr10:99332037-99332325	HUVEC	blood vessel:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
28	RFX5	chr10:99332025-99332379	Hela-S3	cervix:	n/a	n/a
29	YY1	chr10:99332025-99332251	HCT-116	colon:	n/a	n/a
30	ELF1	chr10:99332062-99332251	HepG2	liver:	n/a	n/a
31	CTCF	chr10:99332120-99332270	HCT-116	colon:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
32	RAD21	chr10:99331848-99332601	ECC-1	luminal epithelium:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
33	SMC3	chr10:99331953-99332372	GM12878	blood:	n/a	chr10:99332174-99332188
34	CTCF	chr10:99332100-99332250	HL-60	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
35	RAD21	chr10:99331316-99332653	HCT-116	colon:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
36	SPI1	chr10:99332036-99332375	GM12878	blood:	n/a	n/a
37	CTCF	chr10:99331966-99332376	K562	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
38	CTCF	chr10:99332054-99332311	LNCaP	prostate:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
39	RCOR1	chr10:99332056-99332366	K562	blood:	n/a	n/a
40	RAD21	chr10:99331910-99332432	HepG2	liver:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
41	CTCF	chr10:99332120-99332270	GM12867	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
42	CTCF	chr10:99332100-99332250	HCFaa	heart:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
43	NR3C1	chr10:99332082-99332473	A549	lung:	n/a	chr10:99332389-99332402 chr10:99332316-99332330
44	CTCF	chr10:99332120-99332270	GM12872	blood:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
45	NFIC	chr10:99331852-99332588	ECC-1	luminal epithelium:	n/a	chr10:99332241-99332258 chr10:99332241-99332257
46	CTCF	chr10:99332120-99332270	HRE	kidney:	n/a	chr10:99332175-99332188 chr10:99332173-99332189 chr10:99332172-99332190 chr10:99332174-99332195 chr10:99332175-99332183
47	RAD21	chr10:99331701-99332588	A549	lung:	n/a	chr10:99332173-99332192 chr10:99332322-99332334 chr10:99332178-99332190
48	RAD21	chr10:99332104-99332261	K562	blood:	n/a	chr10:99332173-99332192 chr10:99332178-99332190
49	HMGN3	chr10:99332062-99332515	K562	blood:	n/a	n/a
50	HCFC1	chr10:99332017-99332283	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:99255590..99258774-chr10:99331777..99334688,4	MCF-7	breast:
2	chr10:99222708..99225169-chr10:99331581..99333239,2	MCF-7	breast:
3	chr10:99329733..99337149-chr10:99338392..99346753,19	MCF-7	breast:
4	chr10:99256533..99260506-chr10:99329939..99335950,10	MCF-7	breast:
5	chr10:99205743..99208350-chr10:99330121..99333769,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD2	TF binding region
ENSG00000241935	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000249967	Chromatin interaction
ENSG00000171307	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000171311	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10748698	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10748699	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs10748700	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882956	0.86[ASN][1000 genomes]
rs10882959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10882961	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10882963	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs10882965	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882966	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11189266	0.86[ASN][1000 genomes]
rs11189274	0.90[CEU][hapmap]
rs11189275	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189278	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11189280	0.86[EUR][1000 genomes]
rs11189281	0.87[CHB][hapmap];0.80[JPT][hapmap];0.80[ASN][1000 genomes]
rs11189284	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs11528108	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11528109	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11814566	0.85[CEU][hapmap]
rs12221474	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12243136	0.90[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12357750	0.88[EUR][1000 genomes]
rs1417408	0.90[CEU][hapmap]
rs1475757	0.83[ASN][1000 genomes]
rs1572860	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17108059	0.95[ASN][1000 genomes]
rs3814554	0.90[CEU][hapmap]
rs3818910	0.95[CEU][hapmap]
rs4244325	0.82[EUR][1000 genomes]
rs4244326	0.82[EUR][1000 genomes]
rs4635019	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919104	0.86[CHB][hapmap]
rs7077211	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7089060	0.83[CHB][hapmap]
rs7094973	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs7475470	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7902642	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7921278	0.86[ASN][1000 genomes]
rs7921505	0.86[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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer 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	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99321200-99334600	Weak transcription	HepG2	liver
2	chr10:99322000-99333000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr10:99325600-99334600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr10:99326000-99334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:99326400-99334200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr10:99327000-99334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:99327200-99334600	Weak transcription	Duodenum Mucosa	Duodenum
8	chr10:99327600-99332400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:99327800-99334400	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:99329200-99334000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr10:99329600-99334600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr10:99329800-99333000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr10:99329800-99333000	Enhancers	Esophagus	oesophagus
14	chr10:99329800-99336000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr10:99330000-99335400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:99330200-99332400	Enhancers	HSMMtube	muscle
17	chr10:99330400-99332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr10:99330600-99332400	Enhancers	Brain Angular Gyrus	brain
19	chr10:99330600-99332600	Enhancers	Brain Hippocampus Middle	brain
20	chr10:99330800-99332400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:99330800-99332400	Weak transcription	Aorta	Aorta
22	chr10:99330800-99334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr10:99330800-99334400	Weak transcription	NHLF	lung
24	chr10:99330800-99334600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr10:99330800-99335000	Weak transcription	Ovary	ovary
26	chr10:99330800-99335400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
27	chr10:99330800-99336200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:99330800-99336200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr10:99330800-99336200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr10:99331000-99332600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr10:99331000-99332600	Enhancers	Stomach Mucosa	stomach
32	chr10:99331000-99337200	Enhancers	Fetal Heart	heart
33	chr10:99331200-99332400	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr10:99331200-99332600	Enhancers	Fetal Intestine Small	intestine
35	chr10:99331200-99332800	Enhancers	Brain Anterior Caudate	brain
36	chr10:99331200-99332800	Enhancers	Gastric	stomach
37	chr10:99331200-99333000	Enhancers	Placenta	Placenta
38	chr10:99331200-99334400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr10:99331200-99334400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr10:99331400-99332400	Enhancers	NH-A	brain
41	chr10:99331400-99332600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr10:99331400-99333200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr10:99331400-99336000	Enhancers	Fetal Muscle Leg	muscle
44	chr10:99331400-99336200	Enhancers	Hela-S3	cervix
45	chr10:99331600-99332600	Enhancers	Brain Cingulate Gyrus	brain
46	chr10:99331600-99332600	Genic enhancers	Lung	lung
47	chr10:99331600-99333400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr10:99331800-99332600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr10:99331800-99332600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:99331800-99332800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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