Variant report

Variant	rs34951301
Chromosome Location	chr3:98506109-98506110
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	ATF2	chr3:98505520-98506124	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
3	RUNX3	chr3:98505239-98506188	GM12878	blood:	n/a	n/a
4	NFATC1	chr3:98505347-98506390	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
6	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98504178..98506190-chr3:98512483..98514423,2	MCF-7	breast:
2	chr3:98505121..98508904-chr3:98514678..98518486,3	MCF-7	breast:

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10428160	0.82[EUR][1000 genomes]
rs11552978	0.86[EUR][1000 genomes]
rs12108142	0.89[EUR][1000 genomes]
rs13059624	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13072410	0.89[EUR][1000 genomes]
rs13080057	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13083613	0.86[EUR][1000 genomes]
rs13086148	0.87[AMR][1000 genomes]
rs13091236	0.89[EUR][1000 genomes]
rs13091956	0.87[AMR][1000 genomes]
rs13093128	0.86[EUR][1000 genomes]
rs34470469	0.85[EUR][1000 genomes]
rs35854439	0.82[EUR][1000 genomes]
rs36032715	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs36160001	0.80[EUR][1000 genomes]
rs36175276	0.86[EUR][1000 genomes]
rs41267851	0.91[EUR][1000 genomes]
rs56094988	0.88[EUR][1000 genomes]
rs71311393	0.89[EUR][1000 genomes]
rs71311394	0.89[EUR][1000 genomes]
rs71311397	0.86[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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking 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 target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
12	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
13	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
14	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
20	chr3:98499800-98514800	Weak transcription	Dnd41	blood
21	chr3:98501000-98506600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:98501000-98507400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:98501200-98513400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:98502200-98506200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:98502200-98506600	Genic enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
27	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr3:98502600-98513400	Weak transcription	Fetal Stomach	stomach
30	chr3:98503000-98506400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
31	chr3:98503000-98508000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:98503000-98509200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:98503200-98513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:98503400-98518200	Weak transcription	Ovary	ovary
35	chr3:98503400-98576400	Weak transcription	Gastric	stomach
36	chr3:98503600-98508200	Enhancers	Primary hematopoietic stem cells	blood
37	chr3:98503600-98523800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:98503800-98506200	Enhancers	Osteobl	bone
39	chr3:98503800-98507000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:98503800-98511400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:98504200-98506400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr3:98504600-98506200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:98504600-98506800	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:98504600-98507200	Strong transcription	HUVEC	blood vessel
45	chr3:98504600-98517000	Weak transcription	HSMMtube	muscle
46	chr3:98504600-98519400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
48	chr3:98504800-98514000	Weak transcription	NHEK	skin
49	chr3:98504800-98515000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:98504800-98517400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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