Variant report

Variant	rs10231604
Chromosome Location	chr7:99746201-99746202
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	MAX	chr7:99745989-99747150	H1-hESC	embryonic stem cell:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
2	PBX3	chr7:99745890-99747320	SK-N-SH	brain:	n/a	chr7:99746470-99746490
3	TCF12	chr7:99746062-99746710	A549	lung:	n/a	n/a
4	POLR2A	chr7:99746115-99746873	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr7:99745576-99747499	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr7:99745765-99746742	K562	blood:	n/a	n/a
7	POLR2A	chr7:99746130-99746817	A549	lung:	n/a	n/a
8	TBP	chr7:99746074-99746804	GM12878	blood:	n/a	n/a
9	BACH1	chr7:99746195-99746208	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr7:99745811-99746949	A549	lung:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
11	GABPA	chr7:99746039-99746873	SK-N-SH	brain:	n/a	n/a
12	MAZ	chr7:99746073-99746835	Hela-S3	cervix:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
13	POLR2A	chr7:99746017-99746914	A549	lung:	n/a	n/a
14	MAX	chr7:99745870-99747362	MCF-7	breast:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
15	HA-E2F1	chr7:99746079-99746645	MCF-7	breast:	n/a	n/a
16	HCFC1	chr7:99745930-99747565	Hela-S3	cervix:	n/a	n/a
17	MAX	chr7:99745936-99746846	GM12878	blood:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
18	POLR2A	chr7:99745916-99746993	GM12892	blood:	n/a	n/a
19	TBP	chr7:99746126-99746764	K562	blood:	n/a	n/a
20	CEBPD	chr7:99746178-99746683	HepG2	liver:	n/a	n/a
21	POLR2A	chr7:99746022-99746900	GM12891	blood:	n/a	n/a
22	MAX	chr7:99745973-99746923	ECC-1	luminal epithelium:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
23	RCOR1	chr7:99746110-99746762	HepG2	liver:	n/a	n/a
24	POLR2A	chr7:99745829-99747396	GM12878	blood:	n/a	n/a
25	E2F6	chr7:99745812-99746787	A549	lung:	n/a	n/a
26	POLR2A	chr7:99746055-99746903	HCT-116	colon:	n/a	n/a
27	SIX5	chr7:99745710-99746377	A549	lung:	n/a	n/a
28	MAX	chr7:99745811-99747316	A549	lung:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
29	E2F6	chr7:99745988-99746757	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr7:99746128-99747167	Hela-S3	cervix:	n/a	chr7:99746351-99746361
31	TAF1	chr7:99746153-99746854	K562	blood:	n/a	n/a
32	SPI1	chr7:99746105-99746457	GM12891	blood:	n/a	chr7:99746329-99746336
33	POLR2A	chr7:99746063-99746840	K562	blood:	n/a	n/a
34	POLR2A	chr7:99746032-99747255	A549	lung:	n/a	n/a
35	POLR2A	chr7:99745584-99747320	HepG2	liver:	n/a	n/a
36	MAX	chr7:99746113-99746780	Hela-S3	cervix:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
37	POLR2A	chr7:99745874-99747324	K562	blood:	n/a	n/a
38	SP1	chr7:99746165-99746661	K562	blood:	n/a	chr7:99746350-99746359 chr7:99746471-99746480 chr7:99746349-99746360 chr7:99746469-99746481 chr7:99746351-99746360 chr7:99746351-99746360 chr7:99746349-99746361
39	SMC3	chr7:99746178-99746335	GM12878	blood:	n/a	n/a
40	POLR2A	chr7:99746069-99746865	GM10847	blood:	n/a	n/a
41	POLR2A	chr7:99745856-99747065	U87	brain:	n/a	n/a
42	HMGN3	chr7:99746114-99747154	K562	blood:	n/a	n/a
43	POLR2A	chr7:99745935-99747236	GM12892	blood:	n/a	n/a
44	TAF1	chr7:99746053-99746927	H1-neurons	neurons:	n/a	n/a
45	IRF4	chr7:99746122-99746763	GM12878	blood:	n/a	n/a
46	MAX	chr7:99745960-99746873	ECC-1	luminal epithelium:	n/a	chr7:99746525-99746534 chr7:99746122-99746138
47	ELF1	chr7:99746103-99746865	SK-N-SH	brain:	n/a	chr7:99746398-99746407
48	TBP	chr7:99746182-99746732	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr7:99745934-99747370	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr7:99745994-99747324	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:94799855..94800618-chr7:99746146..99747031,2	HCT-116	colon:
2	chr7:99734202..99739266-chr7:99744673..99748688,7	MCF-7	breast:
3	chr7:99715646..99718646-chr7:99744846..99747972,4	MCF-7	breast:
4	chr12:67663131..67663977-chr7:99745946..99746561,2	NB4	blood:
5	chr7:99723048..99726558-chr7:99745237..99748437,5	K562	blood:
6	chr7:99678150..99680840-chr7:99745802..99747768,2	K562	blood:
7	chr7:99717232..99719759-chr7:99745742..99747993,2	MCF-7	breast:
8	chr7:99722705..99725740-chr7:99745468..99748073,3	K562	blood:
9	chr7:99744806..99746598-chr7:99796497..99798549,2	K562	blood:
10	chr7:99744731..99747065-chr7:100025501..100027244,2	MCF-7	breast:
11	chr7:99745511..99748040-chr7:99809267..99811160,3	MCF-7	breast:
12	chr7:99743864..99749368-chr7:100025322..100029105,6	K562	blood:
13	chr7:99746174..99748056-chr7:99869608..99872452,2	K562	blood:
14	chr7:99723026..99726307-chr7:99744266..99747542,3	MCF-7	breast:
15	chr7:99679340..99681053-chr7:99745802..99747683,2	K562	blood:
16	chr7:99686910..99689525-chr7:99745153..99746949,2	MCF-7	breast:
17	chr7:99744806..99747397-chr7:99797049..99799857,2	K562	blood:

Variant related genes	Relation type
LAMTOR4	TF binding region
ENSG00000078487	Chromatin interaction
ENSG00000180771	Chromatin interaction
ENSG00000106290	Chromatin interaction
ENSG00000111530	Chromatin interaction
ENSG00000214142	Chromatin interaction
ENSG00000271885	Chromatin interaction
ENSG00000242798	Chromatin interaction
ENSG00000160844	Chromatin interaction
ENSG00000214309	Chromatin interaction
ENSG00000166997	Chromatin interaction
ENSG00000239521	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000066923	Chromatin interaction
ENSG00000166526	Chromatin interaction
ENSG00000168090	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11764584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11771167	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12705073	0.85[LWK][hapmap]
rs12878	0.88[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs1527423	0.89[CEU][hapmap];0.88[GIH][hapmap];0.85[TSI][hapmap]
rs1918352	0.83[EUR][1000 genomes]
rs1918353	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.93[EUR][1000 genomes]
rs2272337	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272338	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs2405440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35042434	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736590	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3736591	0.88[GIH][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs3779047	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3800951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3807479	0.82[YRI][hapmap]
rs3823646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4134917	0.86[LWK][hapmap];0.83[YRI][hapmap]
rs4729568	0.83[YRI][hapmap]
rs4729577	0.84[LWK][hapmap];0.83[YRI][hapmap]
rs705867	0.83[LWK][hapmap]
rs7785392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787294	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7787492	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7807641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9649220	0.83[YRI][hapmap]
rs999885	0.85[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap]

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	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv469687	chr7:99572543-99755141	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
5	nsv482601	chr7:99572543-99755141	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1115 gene(s)	inside rSNPs	diseases
6	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
7	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers 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	1085 gene(s)	inside rSNPs	diseases
8	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10231604	TAF6	Cis_1M	lymphoblastoid	RTeQTL
rs10231604	ZSCAN21	cis	parietal	SCAN
rs10231604	ZKSCAN1	cis	multi-tissue	Pritchard
rs10231604	AP4M1	cis	cerebellum	SCAN
rs10231604	AP4M1	cis	Artery Tibial	GTEx
rs10231604	AP4M1	Cis_1M	lymphoblastoid	RTeQTL
rs10231604	AP4M1	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99745400-99746400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr7:99745600-99747000	Active TSS	Brain Substantia Nigra	brain
3	chr7:99745800-99746400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:99745800-99746400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:99745800-99746400	Flanking Active TSS	Primary B cells from cord blood	blood
6	chr7:99745800-99746400	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr7:99745800-99746400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr7:99745800-99746400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr7:99745800-99746400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:99745800-99746400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:99745800-99746400	Flanking Active TSS	Fetal Muscle Trunk	muscle
12	chr7:99745800-99746400	Flanking Active TSS	Fetal Muscle Leg	muscle
13	chr7:99745800-99746400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
14	chr7:99745800-99746400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr7:99745800-99746600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:99745800-99746600	Active TSS	Primary hematopoietic stem cells	blood
17	chr7:99745800-99747000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr7:99745800-99747000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr7:99745800-99747000	Active TSS	Colon Smooth Muscle	Colon
20	chr7:99745800-99747000	Active TSS	Fetal Brain Female	brain
21	chr7:99745800-99747000	Active TSS	Rectal Smooth Muscle	rectum
22	chr7:99745800-99747000	Active TSS	Right Ventricle	heart
23	chr7:99745800-99747200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:99745800-99747200	Active TSS	Brain Cingulate Gyrus	brain
25	chr7:99745800-99747200	Active TSS	Brain Hippocampus Middle	brain
26	chr7:99745800-99747400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr7:99745800-99747400	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr7:99745800-99747400	Active TSS	Fetal Stomach	stomach
29	chr7:99745800-99747600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr7:99745800-99747600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr7:99745800-99747600	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr7:99745800-99747800	Active TSS	Fetal Kidney	kidney
33	chr7:99745800-99748200	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr7:99746000-99746400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr7:99746000-99746400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:99746000-99746400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr7:99746000-99746400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr7:99746000-99746400	Flanking Active TSS	HMEC	breast
39	chr7:99746000-99746600	Active TSS	HepG2	liver
40	chr7:99746000-99746800	Active TSS	Cortex derived primary cultured neurospheres	brain
41	chr7:99746000-99746800	Active TSS	Brain Germinal Matrix	brain
42	chr7:99746000-99747000	Active TSS	Colonic Mucosa	Colon
43	chr7:99746000-99747000	Active TSS	Left Ventricle	heart
44	chr7:99746000-99747200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr7:99746000-99747200	Active TSS	Aorta	Aorta
46	chr7:99746000-99747200	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr7:99746000-99747200	Active TSS	NHLF	lung
48	chr7:99746000-99747400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:99746000-99747400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:99746000-99747400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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