Variant report

Variant	rs2235481
Chromosome Location	chr6:146056848-146056849
allele	A/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	NR2F2	chr6:146056694-146057290	K562	blood:	n/a	n/a
2	CREB1	chr6:146055654-146057365	HepG2	liver:	n/a	n/a
3	SETDB1	chr6:146055807-146057192	K562	blood:	n/a	n/a
4	POLR2A	chr6:146055017-146057985	GM12878	blood:	n/a	n/a
5	MAZ	chr6:146055828-146057530	GM12878	blood:	n/a	chr6:146056754-146056763 chr6:146057245-146057254 chr6:146056754-146056761 chr6:146056752-146056765
6	CBX3	chr6:146056547-146057279	K562	blood:	n/a	n/a
7	PML	chr6:146056239-146056971	MCF-7	breast:	n/a	n/a
8	CTCF	chr6:146056680-146057110	AG04450	lung:	n/a	n/a
9	MYC	chr6:146055787-146057258	Hela-S3	cervix:	n/a	chr6:146056754-146056763 chr6:146057245-146057254 chr6:146056754-146056761 chr6:146056752-146056765
10	POLR2A	chr6:146055809-146056906	A549	lung:	n/a	n/a
11	USF1	chr6:146056551-146056902	A549	lung:	n/a	chr6:146056676-146056692
12	CTCF	chr6:146056780-146056930	GM12873	blood:	n/a	n/a
13	NFIC	chr6:146056576-146057116	HepG2	liver:	n/a	n/a
14	MAX	chr6:146056488-146057235	MCF-7	breast:	n/a	chr6:146056754-146056763 chr6:146056754-146056761 chr6:146056752-146056765
15	POLR2A	chr6:146055778-146056941	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr6:146055648-146057475	GM18505	blood:	n/a	n/a
17	CTCF	chr6:146056720-146056870	HUVEC	blood vessel:	n/a	n/a
18	MXI1	chr6:146056369-146056906	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr6:146055695-146057241	A549	lung:	n/a	chr6:146056134-146056143 chr6:146056078-146056090 chr6:146056683-146056693 chr6:146056820-146056832 chr6:146056229-146056238 chr6:146056640-146056650 chr6:146056079-146056090 chr6:146056008-146056017 chr6:146056237-146056247 chr6:146056246-146056256
20	TBL1XR1	chr6:146056847-146057323	K562	blood:	n/a	n/a
21	MYC	chr6:146055894-146056985	MCF-7	breast:	n/a	chr6:146056754-146056763 chr6:146056754-146056761 chr6:146056752-146056765
22	USF1	chr6:146056614-146056865	A549	lung:	n/a	chr6:146056676-146056692
23	RELA	chr6:146055855-146057366	GM18505	blood:	n/a	n/a
24	BCLAF1	chr6:146055626-146057292	K562	blood:	n/a	chr6:146056929-146056938 chr6:146056638-146056651 chr6:146056681-146056694 chr6:146055898-146055911 chr6:146056643-146056652 chr6:146056085-146056098 chr6:146056635-146056648 chr6:146056640-146056649
25	SMC3	chr6:146056670-146057397	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:146055783-146056886	HepG2	liver:	n/a	n/a
27	MAZ	chr6:146055757-146057140	Hela-S3	cervix:	n/a	chr6:146056754-146056763 chr6:146056754-146056761 chr6:146056752-146056765
28	TBP	chr6:146056796-146057441	Hela-S3	cervix:	n/a	n/a
29	MYBL2	chr6:146055674-146057078	HepG2	liver:	n/a	n/a
30	SIN3A	chr6:146055879-146056856	GM12878	blood:	n/a	n/a
31	SIN3AK20	chr6:146055735-146056939	SK-N-SH	brain:	n/a	n/a
32	ELF1	chr6:146055787-146056978	K562	blood:	n/a	chr6:146056131-146056140 chr6:146056232-146056241 chr6:146056639-146056648 chr6:146056642-146056651 chr6:146056737-146056749
33	TAF1	chr6:146056833-146057280	GM12892	blood:	n/a	n/a
34	POLR2A	chr6:146055475-146057511	H1-hESC	embryonic stem cell:	n/a	n/a
35	HEY1	chr6:146055696-146057362	K562	blood:	n/a	chr6:146056637-146056652 chr6:146055900-146055915 chr6:146056231-146056246 chr6:146056237-146056252
36	CEBPD	chr6:146056760-146057068	HepG2	liver:	n/a	n/a
37	POLR2A	chr6:146055656-146057448	GM12892	blood:	n/a	n/a
38	GABPA	chr6:146055773-146057069	K562	blood:	n/a	chr6:146056007-146056021 chr6:146056636-146056645
39	E2F6	chr6:146055853-146056987	K562	blood:	n/a	chr6:146056134-146056143 chr6:146056078-146056090 chr6:146056683-146056693 chr6:146056820-146056832 chr6:146056229-146056238 chr6:146056640-146056650 chr6:146056079-146056090 chr6:146056008-146056017 chr6:146056237-146056247 chr6:146056246-146056256
40	POLR2A	chr6:146056595-146057319	U87	brain:	n/a	n/a
41	MTA3	chr6:146056447-146057491	GM12878	blood:	n/a	n/a
42	TFAP2C	chr6:146055681-146057097	Hela-S3	cervix:	n/a	n/a
43	MAX	chr6:146055689-146057112	MCF-7	breast:	n/a	chr6:146056754-146056763 chr6:146056754-146056761 chr6:146056752-146056765
44	MTA3	chr6:146056565-146057445	GM12878	blood:	n/a	n/a
45	YY1	chr6:146055794-146057169	GM12891	blood:	n/a	chr6:146056242-146056256 chr6:146056642-146056651 chr6:146056640-146056651 chr6:146056304-146056318 chr6:146056680-146056694 chr6:146055903-146055914 chr6:146056239-146056253 chr6:146056310-146056321 chr6:146056639-146056653 chr6:146056639-146056648 chr6:146056672-146056681 chr6:146056636-146056650
46	E2F4	chr6:146055786-146057293	K562	blood:	n/a	chr6:146056134-146056143 chr6:146056078-146056090 chr6:146056683-146056693 chr6:146056820-146056832 chr6:146056229-146056238 chr6:146056640-146056650 chr6:146056008-146056017 chr6:146056237-146056247 chr6:146056246-146056256
47	POLR2A	chr6:146055791-146056938	A549	lung:	n/a	n/a
48	SIN3AK20	chr6:146056663-146056919	PFSK-1	brain:	n/a	n/a
49	POLR2A	chr6:146055775-146057355	MCF-7	breast:	n/a	n/a
50	TAF1	chr6:146056571-146057220	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:43595203..43596723-chr6:146055866..146057723,2	MCF-7	breast:
2	chr6:146055478..146057329-chr6:146213622..146216410,2	K562	blood:
3	chr6:146054764..146058281-chr6:146133205..146137397,13	MCF-7	breast:
4	chr6:146054881..146058754-chr6:146284576..146286666,3	K562	blood:
5	chr19:55770065..55771348-chr6:146056333..146057332,3	Hela-S3	cervix:
6	chr6:146055814..146058166-chr6:146135376..146138309,3	MCF-7	breast:
7	chr6:146056240..146056988-chr7:100424823..100425448,2	HCT-116	colon:
8	chr6:146056051..146056947-chr9:33025138..33025814,2	Hela-S3	cervix:
9	chr6:146051601..146058492-chr6:146282422..146286666,8	K562	blood:
10	chr1:110950353..110950869-chr6:146056622..146057613,2	Hela-S3	cervix:
11	chr6:146052168..146062191-chr6:146124046..146141258,59	K562	blood:
12	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:
13	chr6:146054743..146057884-chr6:146276241..146279001,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM1-11	chr6:146056706-146058354	ENSG00000270638.1

Variant related genes	Relation type
EPM2A	TF binding region
ENSG00000137074	Chromatin interaction
ENSG00000134248	Chromatin interaction
ENSG00000172432	Chromatin interaction
ENSG00000105063	Chromatin interaction
ENSG00000235652	Chromatin interaction
ENSG00000118496	Chromatin interaction
ENSG00000196411	Chromatin interaction
ENSG00000146414	Chromatin interaction
ENSG00000086061	Chromatin interaction
ENSG00000224699	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1011597	0.89[JPT][hapmap]
rs1070518	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10872580	0.89[JPT][hapmap]
rs11155438	0.89[JPT][hapmap]
rs12199362	0.89[JPT][hapmap];0.82[YRI][hapmap]
rs1292333	0.89[JPT][hapmap]
rs1292334	0.89[JPT][hapmap]
rs1337841	0.89[JPT][hapmap]
rs1415744	0.89[JPT][hapmap]
rs1415746	0.89[JPT][hapmap]
rs1415747	0.89[JPT][hapmap]
rs1890170	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1890171	0.89[JPT][hapmap]
rs1970306	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2050027	0.89[JPT][hapmap]
rs2064185	0.89[JPT][hapmap]
rs2142978	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2142980	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2206142	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2223411	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246132	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2253757	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2265475	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2485631	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34541797	0.85[ASN][1000 genomes]
rs3811102	0.89[JPT][hapmap];0.82[YRI][hapmap]
rs426371	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4398765	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4895683	0.89[JPT][hapmap]
rs4896832	0.89[JPT][hapmap]
rs4896837	0.89[JPT][hapmap]
rs4896838	0.92[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs62435775	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6570701	0.89[JPT][hapmap]
rs6570708	0.89[JPT][hapmap]
rs6570732	0.91[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6900175	0.92[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6901888	0.89[JPT][hapmap]
rs6906258	0.89[JPT][hapmap]
rs6906402	0.89[JPT][hapmap]
rs6915718	0.89[JPT][hapmap]
rs6930154	0.89[JPT][hapmap]
rs6941429	0.89[JPT][hapmap]
rs697053	0.89[JPT][hapmap]
rs697054	0.89[JPT][hapmap]
rs697055	0.89[JPT][hapmap]
rs702304	0.89[JPT][hapmap]
rs702306	0.89[JPT][hapmap]
rs702307	0.89[JPT][hapmap]
rs702316	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs702318	0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs702319	0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs702322	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs702324	0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7752286	0.89[JPT][hapmap]
rs7753273	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753770	0.89[JPT][hapmap]
rs857875	0.89[JPT][hapmap]
rs857877	0.89[JPT][hapmap]
rs857880	0.89[JPT][hapmap]
rs857881	0.89[JPT][hapmap]
rs857882	0.89[JPT][hapmap]
rs857883	0.89[JPT][hapmap]
rs9373467	0.96[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373475	0.89[JPT][hapmap]
rs9376951	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9376961	0.89[JPT][hapmap]
rs9376965	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9386136	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9390356	0.89[JPT][hapmap]
rs9399561	0.89[JPT][hapmap]
rs9403725	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9403737	0.89[JPT][hapmap]
rs9403739	0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs9403749	0.82[YRI][hapmap]
rs9485017	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9497403	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MKK][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9497426	0.83[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3424432	chr6:146041308-146057603	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3471925	chr6:146054784-146057832	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv3471926	chr6:146054784-146057832	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3384876	chr6:146055559-146057657	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146054800-146057800	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:146054800-146058400	Active TSS	Stomach Smooth Muscle	stomach
3	chr6:146055000-146057200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:146055000-146057200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:146055000-146057400	Active TSS	Right Ventricle	heart
6	chr6:146055000-146057600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:146055000-146057600	Active TSS	Colon Smooth Muscle	Colon
8	chr6:146055000-146057800	Active TSS	Brain Angular Gyrus	brain
9	chr6:146055000-146058000	Active TSS	Fetal Stomach	stomach
10	chr6:146055000-146058000	Active TSS	Thymus	Thymus
11	chr6:146055000-146058400	Active TSS	Brain Germinal Matrix	brain
12	chr6:146055000-146058400	Active TSS	Right Atrium	heart
13	chr6:146055200-146057400	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:146055200-146057400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:146055200-146057400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:146055200-146057400	Active TSS	Fetal Thymus	thymus
17	chr6:146055200-146057400	Active TSS	Psoas Muscle	Psoas
18	chr6:146055200-146057400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr6:146055200-146057600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:146055200-146058000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr6:146055200-146058000	Active TSS	Fetal Muscle Leg	muscle
22	chr6:146055200-146058400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:146055400-146057000	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:146055400-146057000	Active TSS	HMEC	breast
25	chr6:146055400-146057200	Active TSS	K562	blood
26	chr6:146055400-146057400	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:146055400-146057400	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr6:146055400-146057400	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr6:146055400-146057400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr6:146055400-146057400	Active TSS	Fetal Intestine Small	intestine
31	chr6:146055400-146057400	Active TSS	Fetal Kidney	kidney
32	chr6:146055400-146057400	Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr6:146055400-146057600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:146055400-146057600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:146055400-146057600	Active TSS	Fetal Intestine Large	intestine
36	chr6:146055400-146057600	Active TSS	Fetal Lung	lung
37	chr6:146055400-146057800	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:146055400-146058000	Active TSS	Rectal Mucosa Donor 31	rectum
39	chr6:146055400-146058000	Active TSS	GM12878-XiMat	blood
40	chr6:146055400-146058400	Active TSS	Brain Anterior Caudate	brain
41	chr6:146055600-146057000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:146055600-146057000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:146055600-146057000	Active TSS	Placenta	Placenta
44	chr6:146055600-146057000	Active TSS	HSMM	muscle
45	chr6:146055600-146057000	Active TSS	NHLF	lung
46	chr6:146055600-146057200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:146055600-146057200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr6:146055600-146057200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:146055600-146057200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:146055600-146057200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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