Variant report

Variant	rs3025643
Chromosome Location	chr6:29569955-29569956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29564780..29575712-chr6:29592511..29597522,14	K562	blood:
2	chr6:29566782..29572750-chr6:29592808..29598864,8	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3095273	0.85[EUR][1000 genomes]
rs3095274	0.86[EUR][1000 genomes]
rs3129034	0.82[AFR][1000 genomes];0.82[AMR][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	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv528285	chr6:29566842-29588146	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv462671	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv601229	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3025643	HIST1H2AB	cis	parietal	SCAN
rs3025643	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29561600-29570000	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:29561600-29570000	Weak transcription	Lung	lung
3	chr6:29561600-29570000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:29561600-29570200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:29561600-29570600	Weak transcription	Right Ventricle	heart
6	chr6:29561600-29571600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:29561800-29570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:29561800-29571600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:29561800-29573200	Weak transcription	HSMMtube	muscle
10	chr6:29562000-29570600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:29562000-29571800	Weak transcription	Left Ventricle	heart
12	chr6:29562000-29572600	Weak transcription	Fetal Heart	heart
13	chr6:29565200-29570200	Weak transcription	Fetal Kidney	kidney
14	chr6:29565600-29570400	Weak transcription	NHDF-Ad	bronchial
15	chr6:29565600-29572200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:29566000-29570000	Weak transcription	NHLF	lung
17	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
18	chr6:29566600-29570200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr6:29566600-29570200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:29566600-29570400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:29566800-29570000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:29566800-29570200	Weak transcription	Adipose Nuclei	Adipose
24	chr6:29566800-29570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:29566800-29570600	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr6:29566800-29570800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:29566800-29570800	Weak transcription	Colon Smooth Muscle	Colon
28	chr6:29566800-29571400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:29566800-29571800	Strong transcription	Fetal Brain Female	brain
30	chr6:29566800-29572000	Weak transcription	Pancreas	Pancrea
31	chr6:29566800-29572400	Weak transcription	HUVEC	blood vessel
32	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:29567000-29570400	Weak transcription	Primary B cells from cord blood	blood
36	chr6:29567000-29570400	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr6:29567000-29571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:29567000-29571200	Weak transcription	Brain Angular Gyrus	brain
39	chr6:29567000-29571800	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:29567200-29571800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:29567200-29571800	Weak transcription	Esophagus	oesophagus
43	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:29567400-29570000	Weak transcription	Brain Cingulate Gyrus	brain
46	chr6:29567400-29570600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:29567400-29572000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr6:29567600-29570200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr6:29567600-29570400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:29567600-29570600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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