Variant report

Variant	rs6975099
Chromosome Location	chr7:98925947-98925948
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:98921655..98927239-chr7:98969297..98973851,7	MCF-7	breast:
2	chr7:98739614..98743126-chr7:98922770..98926033,5	MCF-7	breast:
3	chr7:98925619..98928063-chr7:99006753..99008418,2	MCF-7	breast:
4	chr7:98923496..98925554-chr7:98925570..98927250,2	MCF-7	breast:
5	chr7:98923537..98926194-chr7:98989828..98992452,2	K562	blood:
6	chr7:98921250..98923226-chr7:98924796..98927676,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198742	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106245	Chromatin interaction
ENSG00000130429	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10155966	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10225529	0.87[EUR][1000 genomes]
rs10232076	0.98[ASN][1000 genomes]
rs10236149	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10243678	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10249167	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10255399	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10258757	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10267346	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10270459	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10270917	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10272998	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10274407	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953287	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762273	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17161692	0.98[ASN][1000 genomes]
rs17161695	0.87[EUR][1000 genomes]
rs2072181	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2107922	0.86[EUR][1000 genomes]
rs2286162	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2301889	0.99[ASN][1000 genomes]
rs2404323	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28468623	0.99[ASN][1000 genomes]
rs28495024	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28820905	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3801288	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58660994	0.99[ASN][1000 genomes]
rs59725656	0.97[ASN][1000 genomes]
rs6943920	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6948775	0.98[ASN][1000 genomes]
rs6953476	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6955490	0.81[EUR][1000 genomes]
rs6972337	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73395547	0.99[ASN][1000 genomes]
rs73395557	0.99[ASN][1000 genomes]
rs73395580	0.98[ASN][1000 genomes]
rs9641253	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9768020	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9918551	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6975099	ARPC1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98924200-98926200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:98924400-98926200	Enhancers	Spleen	Spleen
3	chr7:98924400-98926800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr7:98924400-98928000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:98924400-98957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr7:98924600-98926800	Enhancers	Primary B cells from peripheral blood	blood
7	chr7:98924600-98928200	Weak transcription	Esophagus	oesophagus
8	chr7:98924600-98929800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:98924600-98930200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr7:98924600-98971600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr7:98924800-98926000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr7:98924800-98926000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr7:98924800-98926000	Enhancers	Fetal Brain Male	brain
14	chr7:98924800-98926200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:98924800-98926200	Enhancers	Liver	Liver
16	chr7:98924800-98926200	Enhancers	Brain Cingulate Gyrus	brain
17	chr7:98924800-98926400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr7:98924800-98926400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:98924800-98926400	Enhancers	Brain Angular Gyrus	brain
20	chr7:98924800-98926600	Enhancers	Primary T cells fromperipheralblood	blood
21	chr7:98924800-98926600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:98924800-98926600	Enhancers	Lung	lung
23	chr7:98924800-98926600	Enhancers	Pancreas	Pancrea
24	chr7:98924800-98926600	Enhancers	Right Ventricle	heart
25	chr7:98924800-98926800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr7:98924800-98926800	Enhancers	Colon Smooth Muscle	Colon
27	chr7:98924800-98927000	Enhancers	Fetal Heart	heart
28	chr7:98924800-98927400	Enhancers	Brain Hippocampus Middle	brain
29	chr7:98924800-98928400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:98924800-98928400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr7:98924800-98928400	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr7:98924800-98929200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr7:98924800-98929200	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr7:98924800-98930000	Enhancers	Stomach Mucosa	stomach
35	chr7:98924800-98930800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr7:98924800-98930800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr7:98924800-98930800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:98924800-98930800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr7:98924800-98930800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:98924800-98931000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:98924800-98931000	Weak transcription	Fetal Kidney	kidney
42	chr7:98924800-98932600	Weak transcription	Aorta	Aorta
43	chr7:98924800-98935600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr7:98924800-98935600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr7:98924800-98935800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr7:98924800-98936200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr7:98925000-98926200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr7:98925000-98926200	Genic enhancers	Osteobl	bone
49	chr7:98925000-98926400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr7:98925000-98926400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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