Variant report

Variant	rs28429906
Chromosome Location	chr3:195906747-195906748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195871413..195873461-chr3:195905965..195908112,2	K562	blood:
2	chr3:195801020..195810289-chr3:195902611..195915225,28	K562	blood:
3	chr3:195793504..195812987-chr3:195901613..195938073,113	K562	blood:
4	chr3:195903618..195905705-chr3:195906197..195908381,3	K562	blood:
5	chr3:195854603..195857572-chr3:195905057..195907261,2	K562	blood:
6	chr3:195799311..195801331-chr3:195903536..195907265,3	MCF-7	breast:
7	chr3:195865618..195868542-chr3:195904431..195907406,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000252174	Chromatin interaction
ENSG00000072274	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13315288	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2015708	0.88[ASN][1000 genomes]
rs36124256	0.85[ASN][1000 genomes]
rs3850644	0.82[ASN][1000 genomes]
rs3861957	0.84[ASN][1000 genomes]
rs3893275	0.84[ASN][1000 genomes]
rs4916481	0.95[ASN][1000 genomes]
rs4916483	0.96[ASN][1000 genomes]
rs4916491	0.95[ASN][1000 genomes]
rs4916545	0.88[ASN][1000 genomes]
rs62410535	0.95[ASN][1000 genomes]
rs7374788	0.96[ASN][1000 genomes]
rs9325434	0.86[ASN][1000 genomes]
rs9812813	0.83[ASN][1000 genomes]
rs9816881	0.99[ASN][1000 genomes]
rs9824251	0.90[ASN][1000 genomes]
rs9834661	0.89[ASN][1000 genomes]
rs9847725	0.93[ASN][1000 genomes]
rs9855026	0.85[ASN][1000 genomes]
rs9859292	0.96[ASN][1000 genomes]
rs9859624	0.90[ASN][1000 genomes]
rs9869983	0.99[ASN][1000 genomes]
rs9875719	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759213	chr3:195102787-196071593	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	esv2757913	chr3:195379484-196071593	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv532213	chr3:195643944-196063636	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
4	nsv997797	chr3:195658360-196212958	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv878171	chr3:195677895-195959924	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv1008512	chr3:195709662-195974936	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv1002584	chr3:195734933-195910772	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv432543	chr3:195746690-196015690	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv532214	chr3:195762648-195916068	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
10	nsv1009105	chr3:195769609-195984388	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv461130	chr3:195776240-195907653	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv593069	chr3:195776240-195907653	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
13	nsv1005558	chr3:195789462-195919077	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
14	nsv536890	chr3:195789462-195919077	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
15	nsv998042	chr3:195840858-195934070	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1009811	chr3:195851796-196138071	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
17	nsv593070	chr3:195854279-195924203	Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
18	nsv878174	chr3:195858887-195949541	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
19	nsv461131	chr3:195858887-196072442	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
20	nsv593071	chr3:195858887-196072442	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	nsv1004194	chr3:195864466-195919077	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv536891	chr3:195864466-195919077	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1009178	chr3:195864466-196081670	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
24	nsv536892	chr3:195864466-196081670	Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
25	nsv1003550	chr3:195885340-196159824	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
26	nsv536893	chr3:195885340-196159824	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:195897000-195909000	Weak transcription	Spleen	Spleen
2	chr3:195901400-195911800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:195904000-195907200	Enhancers	Fetal Intestine Large	intestine
4	chr3:195904200-195907200	Enhancers	Fetal Intestine Small	intestine
5	chr3:195904400-195907200	Enhancers	Stomach Mucosa	stomach
6	chr3:195904400-195909400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:195904800-195913600	Weak transcription	Right Atrium	heart
8	chr3:195905200-195906800	Weak transcription	Psoas Muscle	Psoas
9	chr3:195905400-195907200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr3:195905400-195907400	Enhancers	Colonic Mucosa	Colon
11	chr3:195905600-195907200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:195905600-195907200	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr3:195905600-195907400	Enhancers	Fetal Brain Male	brain
14	chr3:195905600-195907600	Enhancers	Fetal Muscle Leg	muscle
15	chr3:195905600-195910800	Enhancers	Primary hematopoietic stem cells	blood
16	chr3:195905800-195907000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr3:195905800-195907000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:195906000-195906800	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:195906000-195907200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr3:195906000-195907200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:195906000-195907200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:195906000-195907200	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr3:195906000-195907200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr3:195906000-195907200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr3:195906000-195907200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr3:195906000-195907400	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:195906000-195907600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:195906200-195906800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:195906200-195906800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr3:195906200-195906800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:195906200-195907000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr3:195906200-195907000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:195906200-195907000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr3:195906200-195907000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr3:195906200-195907000	Flanking Active TSS	Brain Substantia Nigra	brain
36	chr3:195906200-195907000	Active TSS	Rectal Smooth Muscle	rectum
37	chr3:195906200-195907000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:195906200-195907000	Bivalent Enhancer	HepG2	liver
39	chr3:195906200-195907000	Enhancers	HUVEC	blood vessel
40	chr3:195906200-195907000	Enhancers	Osteobl	bone
41	chr3:195906200-195907200	Enhancers	H1 Cell Line	embryonic stem cell
42	chr3:195906200-195907200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:195906200-195907200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:195906200-195907200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:195906200-195907200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr3:195906200-195907200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr3:195906200-195907200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:195906200-195907200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:195906200-195907200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:195906200-195907200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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