Variant report

Variant	rs6955891
Chromosome Location	chr7:99035211-99035212
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99035108-99037621	K562	blood:	n/a	n/a
2	POLR2A	chr7:99034966-99035554	HepG2	liver:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99001484..99003635-chr7:99032738..99035703,2	K562	blood:
2	chr7:99034517..99037333-chr7:99070217..99072293,2	K562	blood:
3	chr7:99011715..99014053-chr7:99034853..99036468,2	K562	blood:
4	chr7:99004207..99009187-chr7:99032699..99039268,13	MCF-7	breast:
5	chr7:98970707..98973711-chr7:99034539..99037806,4	MCF-7	breast:
6	chr7:99005761..99007888-chr7:99034840..99036856,3	K562	blood:
7	chr7:99003930..99008101-chr7:99034839..99037079,5	K562	blood:
8	chr7:99010009..99013201-chr7:99032916..99037248,5	MCF-7	breast:
9	chr7:99034720..99038160-chr7:99048984..99054018,5	MCF-7	breast:
10	chr7:98970391..98972681-chr7:99033800..99036309,2	K562	blood:
11	chr7:99004073..99007178-chr7:99034881..99037749,7	MCF-7	breast:
12	chr7:99034954..99037866-chr7:99677567..99679393,3	K562	blood:
13	chr7:99034954..99037975-chr7:99677842..99679932,3	K562	blood:
14	chr7:99034906..99037926-chr7:99095119..99098935,4	K562	blood:
15	chr7:98971332..98973489-chr7:99034701..99036393,2	MCF-7	breast:

No data

Variant related genes	Relation type
CPSF4	TF binding region
PTCD1	TF binding region
ENSG00000166526	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000160908	Chromatin interaction
ENSG00000239133	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000106244	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10215765	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10215854	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226310	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235235	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10236240	1.00[ASN][1000 genomes]
rs10240199	0.82[EUR][1000 genomes]
rs10264505	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10265385	0.82[EUR][1000 genomes]
rs10268984	1.00[ASN][1000 genomes]
rs10273424	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10275381	1.00[ASN][1000 genomes]
rs10277447	1.00[ASN][1000 genomes]
rs10808111	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10808112	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953288	1.00[ASN][1000 genomes]
rs10953289	1.00[ASN][1000 genomes]
rs11555142	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761528	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11766423	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11971640	1.00[ASN][1000 genomes]
rs11973173	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11973801	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974593	1.00[ASN][1000 genomes]
rs11978345	1.00[ASN][1000 genomes]
rs11978582	1.00[ASN][1000 genomes]
rs11980143	1.00[ASN][1000 genomes]
rs11980995	1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	1.00[ASN][1000 genomes]
rs12531852	1.00[ASN][1000 genomes]
rs12533251	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535424	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13227522	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13243267	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17161687	1.00[ASN][1000 genomes]
rs17161761	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003498	1.00[ASN][1000 genomes]
rs28371764	1.00[ASN][1000 genomes]
rs28419687	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602855	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28627543	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34096782	1.00[ASN][1000 genomes]
rs34111611	1.00[ASN][1000 genomes]
rs34257469	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35183025	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35296070	1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45618033	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4765	1.00[ASN][1000 genomes]
rs55761861	1.00[ASN][1000 genomes]
rs57786744	1.00[ASN][1000 genomes]
rs57980352	1.00[ASN][1000 genomes]
rs58964157	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60127638	1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs61740607	1.00[ASN][1000 genomes]
rs66478766	1.00[ASN][1000 genomes]
rs66509940	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66568021	1.00[ASN][1000 genomes]
rs66674233	1.00[ASN][1000 genomes]
rs67279166	1.00[ASN][1000 genomes]
rs67309224	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67860332	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs67934834	1.00[ASN][1000 genomes]
rs6947826	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947941	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947974	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960810	1.00[ASN][1000 genomes]
rs704798	1.00[ASN][1000 genomes]
rs73157587	1.00[ASN][1000 genomes]
rs73157588	1.00[ASN][1000 genomes]
rs73157589	1.00[ASN][1000 genomes]
rs73157590	1.00[ASN][1000 genomes]
rs73157596	1.00[ASN][1000 genomes]
rs73157600	1.00[ASN][1000 genomes]
rs73157601	1.00[ASN][1000 genomes]
rs73157602	1.00[ASN][1000 genomes]
rs73159506	1.00[ASN][1000 genomes]
rs73159509	1.00[ASN][1000 genomes]
rs73159522	1.00[ASN][1000 genomes]
rs73163167	1.00[ASN][1000 genomes]
rs73163169	1.00[ASN][1000 genomes]
rs740160	1.00[ASN][1000 genomes]
rs7778859	1.00[ASN][1000 genomes]
rs868391	1.00[ASN][1000 genomes]
rs9632722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656060	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv888769	chr7:99018584-99041748	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases
6	nsv888770	chr7:99021344-99041748	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6955891	GS1-259H13.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99015600-99035400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:99015600-99035600	Weak transcription	Stomach Mucosa	stomach
4	chr7:99016800-99036000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:99017600-99035600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:99018200-99035400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:99018400-99035600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:99022200-99035400	Weak transcription	NH-A	brain
9	chr7:99023000-99036000	Weak transcription	Small Intestine	intestine
10	chr7:99027200-99035400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr7:99027200-99035600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr7:99028000-99035600	Weak transcription	Primary B cells from cord blood	blood
13	chr7:99031000-99035400	Weak transcription	Fetal Lung	lung
14	chr7:99031400-99035400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr7:99031400-99035400	Weak transcription	Brain Anterior Caudate	brain
16	chr7:99032600-99035400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr7:99032600-99035400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr7:99032800-99035400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:99032800-99035400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr7:99032800-99035400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr7:99032800-99035400	Weak transcription	Colonic Mucosa	Colon
22	chr7:99032800-99035400	Weak transcription	Ovary	ovary
23	chr7:99032800-99035400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr7:99032800-99035600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr7:99032800-99035600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:99032800-99035600	Weak transcription	Left Ventricle	heart
27	chr7:99032800-99035600	Weak transcription	Psoas Muscle	Psoas
28	chr7:99032800-99035600	Weak transcription	Right Ventricle	heart
29	chr7:99033000-99035400	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:99033000-99035400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:99033000-99035400	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:99033000-99035400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr7:99033000-99035400	Weak transcription	Aorta	Aorta
34	chr7:99033000-99035400	Weak transcription	Liver	Liver
35	chr7:99033000-99035400	Weak transcription	Brain Germinal Matrix	brain
36	chr7:99033000-99035400	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:99033000-99035400	Weak transcription	Colon Smooth Muscle	Colon
38	chr7:99033000-99035400	Weak transcription	Gastric	stomach
39	chr7:99033000-99035400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr7:99033000-99035400	Weak transcription	Thymus	Thymus
41	chr7:99033000-99035400	Weak transcription	HSMMtube	muscle
42	chr7:99033000-99035600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:99033000-99035600	Weak transcription	Brain Substantia Nigra	brain
44	chr7:99033000-99035600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr7:99033000-99036000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr7:99033200-99036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:99033400-99035400	Weak transcription	Lung	lung
48	chr7:99033800-99036000	Weak transcription	Spleen	Spleen
49	chr7:99034200-99035600	Weak transcription	Primary T cells from cord blood	blood
50	chr7:99034400-99035400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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