Variant report

Variant	rs7035822
Chromosome Location	chr9:99801875-99801876
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	SMC3	chr9:99801369-99801898	Hela-S3	cervix:	n/a	n/a
2	CTBP2	chr9:99800892-99802098	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr9:99800937-99802003	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr9:99801119-99802062	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3AK20	chr9:99801062-99802214	MCF-7	breast:	n/a	n/a
6	POLR2A	chr9:99801172-99801881	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr9:99801132-99802054	ECC-1	luminal epithelium:	n/a	n/a
8	CREB1	chr9:99801184-99801901	HepG2	liver:	n/a	n/a
9	RAD21	chr9:99800824-99802053	H1-hESC	embryonic stem cell:	n/a	chr9:99801627-99801640
10	RAD21	chr9:99801775-99802132	SK-N-SH_RA	brain:	n/a	n/a
11	SMC3	chr9:99801768-99801876	HepG2	liver:	n/a	n/a
12	POLR2A	chr9:99801024-99802049	H1-hESC	embryonic stem cell:	n/a	n/a
13	SP1	chr9:99801275-99802171	H1-hESC	embryonic stem cell:	n/a	chr9:99801512-99801523 chr9:99801648-99801660 chr9:99801513-99801522 chr9:99801512-99801524 chr9:99801465-99801477 chr9:99801466-99801480 chr9:99801465-99801476 chr9:99801514-99801523 chr9:99801512-99801524 chr9:99801466-99801475 chr9:99801466-99801475 chr9:99801483-99801504 chr9:99801467-99801476
14	POLR2A	chr9:99801174-99802007	HEK293	kidney:	n/a	n/a
15	MXI1	chr9:99800582-99802370	SK-N-SH	brain:	n/a	n/a
16	BHLHE40	chr9:99801251-99802030	K562	blood:	n/a	chr9:99801863-99801879 chr9:99801623-99801639
17	TAF1	chr9:99801142-99801994	ECC-1	luminal epithelium:	n/a	n/a
18	MAZ	chr9:99801254-99802037	K562	blood:	n/a	chr9:99801468-99801478
19	JUND	chr9:99801850-99802050	H1-hESC	embryonic stem cell:	n/a	n/a
20	HCFC1	chr9:99801385-99801932	K562	blood:	n/a	n/a
21	TAF1	chr9:99801000-99802035	ECC-1	luminal epithelium:	n/a	n/a
22	RCOR1	chr9:99801391-99801921	HepG2	liver:	n/a	n/a
23	CREB1	chr9:99801161-99802048	H1-hESC	embryonic stem cell:	n/a	n/a
24	TCF12	chr9:99800996-99802010	ECC-1	luminal epithelium:	n/a	n/a
25	MAX	chr9:99801272-99802057	A549	lung:	n/a	chr9:99801468-99801478
26	POLR2A	chr9:99801125-99802001	HepG2	liver:	n/a	n/a
27	CHD2	chr9:99801181-99802038	HepG2	liver:	n/a	n/a
28	MAX	chr9:99801029-99802220	A549	lung:	n/a	chr9:99801468-99801478
29	POLR2A	chr9:99801409-99802675	K562	blood:	n/a	n/a
30	E2F4	chr9:99801295-99801911	K562	blood:	n/a	chr9:99801480-99801491 chr9:99801467-99801476 chr9:99801630-99801640 chr9:99801494-99801503 chr9:99801464-99801476 chr9:99801481-99801493 chr9:99801463-99801474
31	POLR2A	chr9:99801179-99801894	ECC-1	luminal epithelium:	n/a	n/a
32	POLR2A	chr9:99801456-99801925	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr9:99801800-99801950	HCPEpiC	choroid plexus:	n/a	n/a
34	RAD21	chr9:99801779-99802082	SK-N-SH_RA	brain:	n/a	n/a
35	CHD2	chr9:99801271-99802127	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr9:99801144-99802079	H1-hESC	embryonic stem cell:	n/a	n/a
37	HA-E2F1	chr9:99801240-99802069	MCF-7	breast:	n/a	chr9:99801467-99801476 chr9:99801630-99801640 chr9:99801494-99801503 chr9:99801464-99801476 chr9:99801481-99801493
38	SP4	chr9:99801219-99802058	H1-hESC	embryonic stem cell:	n/a	chr9:99801512-99801523 chr9:99801465-99801481 chr9:99801465-99801476
39	ZNF143	chr9:99801267-99802144	H1-hESC	embryonic stem cell:	n/a	n/a
40	JUND	chr9:99801803-99802102	A549	lung:	n/a	n/a
41	MYC	chr9:99801398-99801929	K562	blood:	n/a	chr9:99801468-99801478
42	SIN3A	chr9:99800563-99802056	H1-hESC	embryonic stem cell:	n/a	chr9:99800969-99800978 chr9:99800941-99800954 chr9:99801633-99801644
43	MAZ	chr9:99800960-99802120	IMR90	lung:	n/a	chr9:99801468-99801478
44	RCOR1	chr9:99801227-99802035	K562	blood:	n/a	n/a
45	MAX	chr9:99801152-99802091	ECC-1	luminal epithelium:	n/a	chr9:99801468-99801478
46	POLR2A	chr9:99801217-99802106	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr9:99801140-99802059	HCT-116	colon:	n/a	n/a
48	SP1	chr9:99801119-99802268	A549	lung:	n/a	chr9:99801512-99801523 chr9:99801648-99801660 chr9:99801513-99801522 chr9:99801512-99801524 chr9:99801149-99801158 chr9:99801465-99801477 chr9:99801466-99801480 chr9:99801465-99801476 chr9:99801514-99801523 chr9:99801512-99801524 chr9:99801466-99801475 chr9:99801466-99801475 chr9:99801483-99801504 chr9:99801467-99801476
49	USF2	chr9:99801358-99802046	H1-hESC	embryonic stem cell:	n/a	chr9:99801863-99801879 chr9:99801623-99801639
50	REST	chr9:99801641-99802128	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:99636633..99638588-chr9:99800511..99803120,2	MCF-7	breast:

Variant related genes	Relation type
CTSV	TF binding region
ENSG00000196597	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10114720	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10115220	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10118886	1.00[ASW][hapmap];0.93[CEU][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10118923	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10123754	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10123757	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10453219	0.85[ASN][1000 genomes]
rs10739289	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10739296	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759389	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10759391	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759399	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10759400	1.00[CEU][hapmap];0.82[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10759406	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759417	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10759420	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10816926	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816951	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10816953	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10816962	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10816963	0.90[EUR][1000 genomes]
rs10816964	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10816981	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816984	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10816994	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10817013	0.82[EUR][1000 genomes]
rs10980241	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10980243	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10980326	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10980346	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10980396	0.81[EUR][1000 genomes]
rs12236690	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12377546	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13299111	0.85[ASN][1000 genomes]
rs15394	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16919034	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34342973	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4367680	0.82[EUR][1000 genomes]
rs4501700	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4510972	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743056	0.85[ASN][1000 genomes]
rs59995818	0.87[EUR][1000 genomes]
rs6477844	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023974	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7038926	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7039198	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7852748	0.85[ASN][1000 genomes]
rs7857836	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7873286	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7875800	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9792463	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053215	chr9:99483926-99824810	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv428540	chr9:99722815-99863455	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv831662	chr9:99752521-99939231	Bivalent Enhancer Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1824305	chr9:99792208-99806169	Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1821221	chr9:99792208-99811206	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7035822	SLC35D2	cis	cerebellum	SCAN
rs7035822	HEMGN	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99800200-99802200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:99800400-99802000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr9:99800400-99802400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:99800600-99802000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:99800600-99802000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr9:99800600-99802000	Active TSS	HSMM	muscle
7	chr9:99800600-99802200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:99800600-99802200	Active TSS	Brain Cingulate Gyrus	brain
9	chr9:99800800-99802000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr9:99800800-99802000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr9:99800800-99802000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:99800800-99802000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr9:99800800-99802000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
14	chr9:99800800-99802000	Active TSS	Fetal Intestine Large	intestine
15	chr9:99800800-99802000	Active TSS	Psoas Muscle	Psoas
16	chr9:99800800-99802000	Active TSS	HSMMtube	muscle
17	chr9:99800800-99802200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr9:99800800-99802200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr9:99800800-99802200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:99800800-99802200	Bivalent/Poised TSS	Fetal Kidney	kidney
21	chr9:99800800-99802200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr9:99800800-99802400	Active TSS	A549	lung
23	chr9:99801000-99802000	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr9:99801000-99802000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr9:99801000-99802000	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:99801000-99802000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr9:99801000-99802000	Flanking Active TSS	Adipose Nuclei	Adipose
28	chr9:99801000-99802000	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr9:99801000-99802000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
30	chr9:99801000-99802000	Flanking Active TSS	Placenta	Placenta
31	chr9:99801000-99802000	Active TSS	Rectal Smooth Muscle	rectum
32	chr9:99801000-99802000	Active TSS	NHDF-Ad	bronchial
33	chr9:99801000-99802200	Active TSS	H1 Cell Line	embryonic stem cell
34	chr9:99801000-99802200	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr9:99801000-99802200	Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr9:99801000-99802200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr9:99801000-99802200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr9:99801000-99802200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:99801000-99802200	Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr9:99801000-99802200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:99801000-99802200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:99801000-99802200	Active TSS	Fetal Intestine Small	intestine
43	chr9:99801000-99802400	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr9:99801200-99802000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr9:99801200-99802000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
46	chr9:99801200-99802000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:99801200-99802200	Active TSS	ES-I3 Cell Line	embryonic stem cell
48	chr9:99801200-99802200	Active TSS	Placenta Amnion	Placenta Amnion
49	chr9:99801200-99802200	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr9:99801200-99802400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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