Variant report

Variant	rs6702891
Chromosome Location	chr1:153540186-153540187
allele	A/C
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	chr1:153540123-153541730	HCT-116	colon:	n/a	chr1:153541178-153541196 chr1:153541180-153541193 chr1:153541173-153541194 chr1:153541143-153541152 chr1:153541181-153541191 chr1:153541143-153541156 chr1:153541184-153541193 chr1:153541179-153541195
2	TFAP2C	chr1:153540146-153541439	Hela-S3	cervix:	n/a	n/a
3	SMC3	chr1:153540099-153541500	Hela-S3	cervix:	n/a	chr1:153541187-153541194 chr1:153541180-153541194
4	FOS	chr1:153540047-153540587	MCF10A-Er-Src	breast:	n/a	n/a
5	NR3C1	chr1:153540027-153540550	A549	lung:	n/a	chr1:153540168-153540175
6	MYC	chr1:153540086-153541469	MCF10A-Er-Src	breast:	n/a	chr1:153540434-153540445
7	MAX	chr1:153540007-153541488	ECC-1	luminal epithelium:	n/a	chr1:153540434-153540445
8	STAT3	chr1:153540074-153540507	MCF10A-Er-Src	breast:	n/a	chr1:153540337-153540349
9	CTCF	chr1:153540040-153540190	SAEC	small airway:	n/a	n/a
10	EP300	chr1:153540085-153541571	A549	lung:	n/a	n/a
11	NR2F2	chr1:153539999-153541569	MCF-7	breast:	n/a	n/a
12	MAX	chr1:153540152-153541488	Hela-S3	cervix:	n/a	chr1:153540434-153540445
13	SP1	chr1:153539996-153541590	HCT-116	colon:	n/a	chr1:153540265-153540272
14	SIN3AK20	chr1:153540125-153541362	A549	lung:	n/a	n/a
15	RAD21	chr1:153540154-153541382	A549	lung:	n/a	chr1:153541182-153541191 chr1:153541179-153541192 chr1:153541176-153541195 chr1:153541180-153541190 chr1:153541180-153541194
16	CTCF	chr1:153540029-153541699	A549	lung:	n/a	chr1:153541178-153541196 chr1:153541180-153541193 chr1:153541173-153541194 chr1:153541143-153541152 chr1:153541181-153541191 chr1:153541143-153541156 chr1:153541184-153541193 chr1:153541179-153541195
17	TCF7L2	chr1:153540150-153541468	Hela-S3	cervix:	n/a	chr1:153540190-153540197
18	STAT3	chr1:153540166-153540515	MCF10A-Er-Src	breast:	n/a	chr1:153540337-153540349
19	POLR2A	chr1:153539984-153541448	Hela-S3	cervix:	n/a	n/a
20	MAZ	chr1:153540013-153541653	IMR90	lung:	n/a	chr1:153540434-153540445
21	TCF12	chr1:153540170-153540800	ECC-1	luminal epithelium:	n/a	n/a
22	FOS	chr1:153540137-153540648	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr1:153540135-153540513	MCF10A-Er-Src	breast:	n/a	chr1:153540337-153540349
24	SMARCC1	chr1:153540091-153541383	Hela-S3	cervix:	n/a	chr1:153540311-153540320
25	RAD21	chr1:153540093-153541587	HCT-116	colon:	n/a	chr1:153541182-153541191 chr1:153541179-153541192 chr1:153541176-153541195 chr1:153541180-153541190 chr1:153541180-153541194
26	MAFK	chr1:153540181-153541482	Hela-S3	cervix:	n/a	chr1:153541290-153541300 chr1:153541290-153541299
27	POLR2A	chr1:153540061-153541529	HCT-116	colon:	n/a	n/a
28	RAD21	chr1:153539988-153541687	HCT-116	colon:	n/a	chr1:153541596-153541606 chr1:153541182-153541191 chr1:153541179-153541192 chr1:153541176-153541195 chr1:153541180-153541190 chr1:153541180-153541194
29	MAX	chr1:153537764-153541614	A549	lung:	n/a	chr1:153540434-153540445
30	POLR2A	chr1:153540014-153541528	Hela-S3	cervix:	n/a	n/a
31	SMC3	chr1:153539993-153541754	SK-N-SH	brain:	n/a	chr1:153541187-153541194 chr1:153541180-153541194
32	SP1	chr1:153540172-153541565	A549	lung:	n/a	chr1:153540265-153540272
33	RAD21	chr1:153540163-153541507	Hela-S3	cervix:	n/a	chr1:153541182-153541191 chr1:153541179-153541192 chr1:153541176-153541195 chr1:153541180-153541190 chr1:153541180-153541194
34	JUN	chr1:153540180-153541465	Hela-S3	cervix:	n/a	n/a
35	MAZ	chr1:153540177-153541474	Hela-S3	cervix:	n/a	chr1:153540434-153540445
36	POLR2A	chr1:153540040-153541582	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:153539984-153541364	Hela-S3	cervix:	n/a	n/a
38	GTF2F1	chr1:153540147-153541445	Hela-S3	cervix:	n/a	n/a
39	FOSL2	chr1:153539998-153540710	A549	lung:	n/a	n/a
40	MAX	chr1:153539995-153541489	A549	lung:	n/a	chr1:153540434-153540445
41	POLR2A	chr1:153540130-153541564	HCT-116	colon:	n/a	n/a
42	TCF12	chr1:153537752-153541616	A549	lung:	n/a	chr1:153539098-153539108 chr1:153537891-153537901 chr1:153541146-153541156 chr1:153539241-153539251
43	CHD2	chr1:153540156-153541438	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr1:153540035-153540259	MCF-7	breast:	n/a	n/a
45	MYC	chr1:153540070-153541478	MCF10A-Er-Src	breast:	n/a	chr1:153540434-153540445
46	SMARCB1	chr1:153540038-153541423	Hela-S3	cervix:	n/a	chr1:153540311-153540320
47	FOS	chr1:153540060-153541487	MCF10A-Er-Src	breast:	n/a	chr1:153541290-153541301
48	EP300	chr1:153540102-153541468	A549	lung:	n/a	n/a
49	FOSL1	chr1:153537724-153541695	HCT-116	colon:	n/a	chr1:153539206-153539216 chr1:153539205-153539217 chr1:153539169-153539178 chr1:153539207-153539215 chr1:153539208-153539219 chr1:153539206-153539216 chr1:153538365-153538374 chr1:153538361-153538372 chr1:153539206-153539216 chr1:153539205-153539216 chr1:153539167-153539178
50	TCF7L2	chr1:153540071-153541466	HCT-116	colon:	n/a	chr1:153540190-153540197

No.	Distal block	Cell Line	Cell type
1	chr1:153538054..153540599-chr1:153598556..153600339,3	K562	blood:
2	chr1:153535304..153546939-chr1:153598248..153612195,40	MCF-7	breast:
3	chr1:153537679..153540436-chr1:153962275..153964884,2	K562	blood:
4	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
5	chr1:153533881..153554060-chr1:153575339..153590405,58	MCF-7	breast:
6	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:
7	chr1:153537973..153540755-chr1:153602282..153604926,2	K562	blood:
8	chr1:153539289..153541606-chr1:153604560..153606747,2	K562	blood:
9	chr1:153517686..153519228-chr1:153538736..153541189,3	K562	blood:
10	chr1:153516187..153518294-chr1:153538747..153540345,2	K562	blood:
11	chr1:153539321..153541162-chr1:153580987..153583409,2	K562	blood:
12	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
13	chr1:153539127..153551919-chr1:153598146..153608314,34	MCF-7	breast:
14	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
15	chr1:153534464..153536760-chr1:153538176..153540228,3	MCF-7	breast:
16	chr1:153536449..153542914-chr1:153579157..153590800,34	MCF-7	breast:
17	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
18	chr1:153327681..153330764-chr1:153538971..153541656,5	MCF-7	breast:
19	chr1:153536608..153541746-chr1:153698648..153702694,5	MCF-7	breast:
20	chr1:153537634..153542525-chr1:153598837..153602183,9	K562	blood:

Variant related genes	Relation type
S100A2	TF binding region
ENSG00000143624	Chromatin interaction
ENSG00000188015	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000199565	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000160678	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000197956	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1047325	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs1050923	0.90[GIH][hapmap]
rs11488669	0.90[GIH][hapmap]
rs16835437	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs16835455	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28689606	1.00[ASN][1000 genomes]
rs3762268	0.90[GIH][hapmap]
rs4595398	0.90[GIH][hapmap]
rs55955983	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56057245	1.00[ASN][1000 genomes]
rs60069797	1.00[ASN][1000 genomes]
rs61558997	1.00[ASN][1000 genomes]
rs6671398	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6703014	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8401	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
4	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153535800-153540800	Enhancers	Fetal Muscle Leg	muscle
2	chr1:153535800-153541600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:153536000-153540800	Enhancers	Fetal Muscle Trunk	muscle
4	chr1:153536000-153541600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:153536000-153541600	Enhancers	Placenta	Placenta
6	chr1:153536000-153541600	Enhancers	Lung	lung
7	chr1:153536000-153542000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153536200-153541800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:153536600-153541000	Enhancers	Fetal Intestine Large	intestine
10	chr1:153536800-153540800	Enhancers	Stomach Mucosa	stomach
11	chr1:153536800-153541800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:153537000-153540800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:153537000-153541600	Enhancers	HUVEC	blood vessel
14	chr1:153537600-153541600	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:153537800-153540400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:153537800-153540400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:153537800-153540400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:153537800-153540400	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr1:153537800-153540600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:153537800-153540600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr1:153537800-153540800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr1:153537800-153540800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr1:153537800-153540800	Enhancers	Right Ventricle	heart
24	chr1:153537800-153540800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr1:153537800-153541000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr1:153537800-153541000	Enhancers	Primary B cells from cord blood	blood
27	chr1:153537800-153541600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:153537800-153541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr1:153537800-153541600	Enhancers	Fetal Heart	heart
30	chr1:153537800-153541600	Enhancers	Fetal Thymus	thymus
31	chr1:153537800-153541800	Flanking Active TSS	Hela-S3	cervix
32	chr1:153538000-153540400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr1:153538000-153540800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:153538000-153540800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr1:153538000-153540800	Enhancers	Fetal Kidney	kidney
36	chr1:153538000-153541000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr1:153538000-153541000	Enhancers	Right Atrium	heart
38	chr1:153538000-153541200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:153538000-153541200	Enhancers	Psoas Muscle	Psoas
40	chr1:153538000-153541400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:153538000-153541400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:153538000-153541400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr1:153538000-153541400	Enhancers	Left Ventricle	heart
44	chr1:153538000-153541600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:153538000-153541600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:153538200-153540600	Enhancers	Brain Hippocampus Middle	brain
47	chr1:153538200-153540800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr1:153538200-153540800	Enhancers	Pancreas	Pancrea
49	chr1:153538200-153541000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:153538200-153541000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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